Load Libraries

# libraries used for analysis
library(edgeR)
library(limma)
library(quadprog)
library(ruv)

# libraries required for graphics
library(ggplot2)
library(reshape2)
library(EDASeq)
library(RColorBrewer)
library(VennDiagram)
library(data.table)
library(dplyr)
library(stringr)
library(knitr)
library(pheatmap)


wd = "./"
colors <- c("#0571b0", "#ca0020")

Load our data

We first produce a matrix of read counts after aligning to both the Human and Plasmodium falciparum 3D7 reference genome. Subread’s featureCounts program is then used to allocate reads to gene features using the gff file PlasmoDB-12.0_Pfalciparum3D7.gff from PlasmoDB. For both Subread programs the default options are used.

setwd(wd)
# # Next subreads featureCounts was used to allocate reads to genes. This
# was saved for re-use files <-
# Sys.glob('/home/users/allstaff/tonkin-hill.g/all_gene_analysis/alignment/*.sam')
# fc_genes_aligned_w_Pfhuman_withoutVivax <- featureCounts(files, annot.ext
# = './data/PlasmoDB-12.0_Pfalciparum3D7.gff' , isPairedEnd=TRUE,
# isGTFAnnotationFile=TRUE, GTF.attrType='ID', GTF.featureType='gene' ,
# nthreads=15)

# Load gene ID mappings which we use later on.
geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)
trim <- function(x) gsub("^\\s+|\\s+$", "", x)
s <- str_split(as.character(geneID_mappings$`[Previous ID(s)]`), ",")
geneID_mappings <- data.frame(current = rep(geneID_mappings$`[Gene ID]`, sapply(s, 
    FUN = length)), old = unlist(s))
geneID_mappings$old <- str_trim(geneID_mappings$old)

# Load read counts (if featureCounts has been run previously)
load("./data/fc_genes_with_all_samples_aligned_human_Pf_WithOutVivax_subread_uH.RData")
fc2 <- fc_genes_aligned_w_Pfhuman_withoutVivax
t <- fc2$counts

# Rename samples to something more sensible colnames(t) <-
# gsub('alignment\\.sam','',colnames(t)) colnames(t) <-
# gsub('.*vivax\\.','',colnames(t)) colnames(t) <- gsub('_S.*','',
# colnames(t))
fc2$counts <- t

x <- DGEList(counts = fc2$counts, genes = fc2$annotation)

Initial filter

We next filter out genes that do not have sufficient coverage across our samples for reliable estimates to be made.

setwd(wd)
before <- nrow(x$counts)
keep <- rowSums(cpm(x) > 2) >= 10
x <- x[keep, , keep.lib.sizes = FALSE]

We require that there are at least 2 reads per million for at least 10 samples in order for a gene to be included in the analysis. This reduced the number of genes being considered from 5777 to 4144.

Remove low depth samples

setwd(wd)
bplot <- melt(colSums(x$counts))
colnames(bplot) <- c("Read.Counts")
bplot$Sample <- rownames(bplot)

gg <- ggplot(bplot, aes(x = factor(Sample), y = Read.Counts)) + geom_bar(stat = "identity")
gg <- gg + theme_bw() + scale_y_sqrt(breaks = c(0, 10000, 1e+06, 1e+07, 1e+08))
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"))
gg <- gg + labs(x = "Sample", y = "Read Count")
gg <- gg + geom_hline(aes(yintercept = 1e+06), col = "red")

x$counts <- x$counts[, !grepl("SFD1|SFM9|SFC\\.025", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

gg

Samples SFD1, SFM9 and SFC.025 were not sequenced to a sufficient depth to be reliable and thus are removed.

Remove drug treated samples

Samples SFU2 and SFU3 were drug treated and are removed.

x$counts <- x$counts[, !grepl("SFU2|SFU\\.3", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

Now we take the log transform of our sample counts (RPKM) to estimate the proportion of different stages present.

setwd(wd)
our_log_rpkm <- rpkm(dge)
our_log_rpkm <- log2(1 + our_log_rpkm)

Estimate Contributions from Different Life-cycle Stages

Load Data

To estimate the proportion of different life-cycle stages in each of our samples we require a reference data set. Su et al provide such a reference. They performed RNA-seq at two gametocyte stages, an ookinete stage and four time points of erythrocytic stages representing ring, early trophozoite, late trophozoite, and schizont. As we do not expect any ookinete stage parasites we discarded this reference. The data was downloaded from PlasmoDB and as such read counts were reported in RPKM. To handle outlying counts in a sensible manner a log2 transformation of the RPKM values was performed. This was also done for our gene counts. By next fitting a mixture model we can estimate the proportion of different parasite stages that make up our samples.

setwd(wd)
su_rpkm <- read.csv("./data/ rpkm_7SexualAndAsexualLifeStages_suetal.csv", header = TRUE, 
    sep = ",")

# ignore the Ookinete profile as this should be absent from our data.
su_rpkm$Ookinete <- NULL
rownames(su_rpkm) <- su_rpkm$ID
su_rpkm$ID <- NULL

# take the log transform of the data which helps to manage outlier genes.
su_log_rpkm <- log2(1 + su_rpkm)

Mixture Model

Given a set of stages \(S\) and a set of genes \(g_i: i\in \{1,...,N\}\) we want to minimise

\[ \sum_{i=1}^N \left( g_{i,sample} - \sum_{s \in S} \pi_s g_{i,s} \right)^2 \]

Subject to constraints

\[ \sum_{s\in S} \pi_s = 1 \]

\[ \pi_s > 0 \]

Here \(\pi_s\) is proportion of stage \(s\) that is attributed to having contributed to our sample. This model was fit using R’s solve.QP function.

setwd(wd)
findMix <- function(Y, X) {
    X[is.na(X)] <- t(replicate(ncol(X), apply(X, 1, mean, na.rm = T)))[is.na(X)]
    Rinv <- solve(chol(t(X) %*% X))
    C <- cbind(rep(1, ncol(X)), diag(ncol(X)))
    b <- c(1, rep(0, ncol(X)))
    d <- t(Y) %*% X
    qp <- solve.QP(Dmat = Rinv, factorized = TRUE, dvec = d, Amat = C, bvec = b, 
        meq = 1)
    sol <- qp$solution
    sol[sol < 1e-10] <- 0
    return(sol)
}

Calculate Sample Life-Cycle Profiles

We fit this mixture model to each of our samples in turn. The results are then plotted. A column represents each sample in the plot below. As we are fitting proportion parameters each columns values must add to 1 over the 5 stages. Note that we have also combined the estimated proportions for the gametocyte samples into one gametocyte variable. The columns are coloured by phenotype.

setwd(wd)
# First get the intersection of the genes for the two datasets and order
# them by rowname.
inter <- intersect(rownames(our_log_rpkm), rownames(su_log_rpkm))

O <- our_log_rpkm[rownames(our_log_rpkm) %in% inter, ]
O <- O[order(rownames(O)), ]
S <- su_log_rpkm[rownames(su_log_rpkm) %in% inter, ]
S <- S[order(rownames(S)), ]

# Now lets fit some samples!
ourPlotData <- data.frame()
for (i in 1:ncol(O)) {
    mix <- findMix(O[, i], as.matrix(S))
    ourPlotData <- rbind(ourPlotData, data.frame(sample = rep(colnames(O)[i], 
        ncol(S)), stage = colnames(S), proportion = mix))
}

# Organise the results.
ourPlotData$stage <- gsub("Gametocyte.*", "Gametocyte", ourPlotData$stage)
ourPlotData <- aggregate(proportion ~ sample + stage, data = ourPlotData, FUN = sum)
ourPlotData <- within(ourPlotData, stage <- factor(stage, levels = c("Ring", 
    "Early.Trophozoite", "Late.Trophozoite", "Schizont", "Gametocyte")))
ourPlotData$phenotype <- ifelse(substring(ourPlotData$sample, 1, 1) == "I", 
    "non-severe", "severe")

# Make a pretty plot.
gg <- ggplot(ourPlotData, aes(x = factor(sample), y = proportion, fill = factor(phenotype))) + 
    geom_bar(stat = "identity")
gg <- gg + scale_fill_manual(values = c(`non-severe` = "#2c7bb6", severe = "#d7191c"))
gg <- gg + facet_wrap(~stage, ncol = 1)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"), strip.text.x = element_text(size = 16, 
    face = "bold"))
gg <- gg + labs(x = "Sample", y = "Proportion", fill = "Stage")
gg <- gg + theme(legend.text = element_text(size = 14))
gg <- gg + theme(legend.key.size = unit(0.25, "in"))
gg <- gg + theme(legend.title = element_text(size = 16, face = "bold"))
gg <- gg + guides(fill = guide_legend(title = "Phenotype"))
gg

Investigate Differential Expression

We now perform the Voom transformation on our count matrix. Prior to the transformation we use TMM normalisation to account for the different library sizes present in our sample. TMM was chosen as it is more robust to outliers. From the Voom variance trend it is evident that there are a number of genes that have both high variability and high expression. After looking at some of the main offenders these were identified to be influenced by staging in the parasite. Consequently it is important to account for life-cycle stage when conducting the differential expression analysis.

options(width = 150)
setwd(wd)
categories <- as.factor(substring(rownames(dge$samples), 1, 1))
dge <- calcNormFactors(dge, method = "TMM")
dge$samples$group <- categories
design <- model.matrix(~group, data = dge$samples)

v <- voom(dge, design = design, plot = TRUE)

PCA Normalising for Library Size

The PCA plot below indicates that accounting for library size alone does not cope with the impact of life-cycle stages. Notably SFC21 is clearly an outlier and was identified in the mixture model as containing later stage parasites as well as gametocytes. IFM14 is also slightly separate in the PCA plot and was identified as having a proportion of Schizont stage parasite present.

setwd(wd)
plotPCA(v$E, col = colors[categories], cex = 0.8, isLog = TRUE)

Further the Relative Log Expression (RLE) plot below suggests that there is something different about SFC21 as well as highlighting IFM060 as being different.

setwd(wd)
plotVoomRLE <- function(E, colours) {
    mn <- apply(E, 1, median)
    rle <- data.frame(sweep(E, MARGIN = 1, STATS = mn, FUN = "-"))
    boxplot(rle, col = colours, outline = FALSE, las = 2, ylim = c(-7, 7))
    abline(h = 0, col = "black")
}
plotVoomRLE(v$E, colors[categories])

PCA Normalising for Library Size, Ring, Gametocyte and Schizont effects.

To investigate the impact of life-cycle stages in our analysis we fit a linear model using limma’s removeBatchEffect. Initially ring, gametocyte and schizont parameters were fit along with the disease phenotype factor. This was because for the most part the Trophozoite stages could be represented by accounting for these stages as they would be present implicitly in the model.

The PCA indicates that we have dealt with the outlying SFC21 sample as well as other less outlying samples such as IFM14 which showed a proportion of Schizont stage parasites in the mixture model. Unfortunately due to the low number of samples that have proportions of Schizont and Gametocytes estimating differential differential expression in severe disease becomes impossible. This is because there is insufficient data to estimate these stage parameters and consequently the uncertainty in the model is too high to find significant differences between severe and non-severe disease.

setwd(wd)
covs <- data.frame(v$design[, 2])
ourPlotData$phenotype <- NULL
c <- dcast(ourPlotData, sample ~ ..., value.var = "proportion")
covs <- merge(covs, c, by.x = 0, by.y = "sample")

colnames(covs) <- c("sample", "disease", colnames(c)[2:ncol(c)])
rownames(covs) <- covs$sample
covs$sample <- NULL
covs <- covs[match(colnames(v$E), rownames(covs)), ]
stopifnot(colnames(v$E) == rownames(covs))
# head(covs)

covs <- covs[, c(1, 2, 5, 6)]
# head(covs)

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also suggests we have dealt with SFC21 however accounting for these stages does not seem to have accounted for the differences we see in the IFM060 sample. The mixture model did not identify IFM060 as being noticeably different from the other samples and consequently it is likely that there is some other unknown factor impacting on its expression.

setwd(wd)
plotVoomRLE(norm_counts_ring, col = colors[categories])

PCA Normalising for Library Size and Ring Stage Effects

We then investigate the impact of only accounting for the Ring stage parameter in the model. This gives us more power with which to identify differential expression related to severe disease. However, from the PCA plot below it is clear that accounting for Ring stage alone is insufficient and fails to adequately deal with SFC21.

setwd(wd)
covs <- covs[, c(1, 2)]

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

We are however able to identify differentially expressed genes in this less parameterised model. The summary of results accounting only for the Ring stage variable are given below. This test was performed using the limma-Voom pipeline. Ideally we would be able to keep both the power in out tests and account for the remaining unwanted factors. To achieve this we make use of RUV-4 to estimate dummy variables that represent multiple unknown factors of unwanted variation.

setwd(wd)
stopifnot(colnames(dge) == rownames(mod))
v2 <- voom(dge, design = mod, plot = FALSE)
fit <- lmFit(v2, mod)
fit <- eBayes(fit, robust = TRUE)

summary(de1 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))
##    (Intercept) disease Ring
## -1          85      58 1295
## 0          645    3939 1672
## 1         3414     147 1177

Estimate Unwanted Factors of Variation

To cope with the outlier samples such as SFC21 whilst retaining statistical power we estimate factors of unwanted variation using RUV-4.
RUV-4 requires a set of control genes which are believed to be relatively unaffected by the condition of interest, in our case this is disease severity. RUV-4 is however fairly robust to the choice of control genes.
We chose to use the 1000 genes found to have the highest p-values in the experiment of Vignali et al as controls. The experiment of Vignali et al looked at differences in expression between pregnancy associated malaria and childhood malaria. Although this is not the same association we are investigating it was considered close enough to perform adequately as a source of control genes. Further an analysis using SVA which does not require controls and rather estimates them empirically was found to produce similar results with only 5 out of 119 genes found using SVA missing from the RUV-4 approach. Further RUV-4 attempts to recover some variation that may be lost in the vanilla SVA approach when the factor of interest (severe disease) correlates with an unwanted factor. Consequently it leads to a higher number of differentially expressed genes being found. It was also thought that having an independently sourced set of control genes was preferable to empirically deriving such a set.

setwd(wd)
contol_genes_vignali <- read.table("./data/contol_genes_vignali.txt", quote = "\"")

ctrl_vignali <- geneID_mappings$current[geneID_mappings$old %in% contol_genes_vignali$V1]
length(ctrl_vignali)
## [1] 1009
empirical_controls <- ctrl_vignali[0:length(ctrl_vignali)]
empirical_controls <- rownames(v$E) %in% empirical_controls

categoriesRUV <- categories
categoriesRUV <- data.matrix(as.numeric(categoriesRUV == "S"))
ring <- data.matrix(mod[, c(1, 3)])
genes <- data.matrix(t(v$E))

ruv <- RUV4(genes, categoriesRUV, empirical_controls, 3, Z = ring)

modRUV = cbind(mod, ruv$W)

norm_counts_ring_ruv <- removeBatchEffect(v$E, covariates = modRUV[, 3:ncol(modRUV)], design = modRUV[, 1:2])

Note that although we used 1000 genes from the experiment of Vignali et al only 533 were found in our reduced expression matrix.

The PCA plot below indicates that we have dealt with most of the problems due to staging. Here we have included the Ring stage proportion from the mixture model as well as three factors of unwanted variation estimated using RUV-4.

setwd(wd)
plotPCA(norm_counts_ring_ruv, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also indicates that we have succesfully dealt with most of the staging issues. Both SFC21 and IFM14 have reasonable box plots. Moreover, IFM060 has a nicer boxplot indicating that in using RUV-4, not only have we dealt with staging issues, we have also accounted for some other unknown confounding factors that would have impacted our results. The variation in each sample has also been reduced which is indicated in the reduced height of the boxplot whiskers. Finally, the results were found to be relatively robust to the removal of the outlier samples such as SFC21 and IFM14. Consequently, this approach seems to succesfully deal with both life-cycle staging issues and other unknown impacting factors.

setwd(wd)
plotVoomRLE(norm_counts_ring_ruv, colors[categories])

Identify DE Genes using Limma and Voom

We now use the limma-voom pipeline, with the robust ebayes option which handles dispersion outliers. This was done to further ensure our results were less likely to be affected by outlier samples. Multiple testing correction was performed using the Benjamini-Hochberg approach.

setwd(wd)
stopifnot(colnames(dge) == rownames(modRUV))
v2 <- voom(dge, design = modRUV, plot = F)
fit <- lmFit(v2, modRUV)
fit <- eBayes(fit, robust = TRUE)
s <- summary(de2 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))
s
##    (Intercept) disease Ring               
## -1          94     153 1391 1682 1143  545
## 0          521    3873 1429 1579 1870 2954
## 1         3529     118 1324  883 1131  645

Overall 271 genes were found to be differentially expressed between severe and non-severe cases of malaria with a false dicovery rate threshold of 0.05.

A good check for validity of our model it to look at the distribution of the resulting p-values. If everything is okay we would expect a uniform distribution except near \(p=0\) where we would hope to see a spike. The barplot below indicates this is what we see which is helpful in affirming that we have done okay in removing unwanted variation without negatively impacting on the variation due to the variable of interest (diseas severity).

setwd(wd)
top_ring_ruv <- topTable(fit, coef = 2, p.value = 0.1, sort.by = "p", number = Inf, adjust.method = "BH", confint = TRUE)
hist <- data.frame(topTable(fit, coef = 2, number = Inf))
gg <- ggplot(hist, aes(x = P.Value)) + geom_histogram(binwidth = 0.01)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12), axis.text.y = element_text(size = 12, angle = 0), axis.title = element_text(size = 12, face = "bold"))
gg <- gg + labs(x = "P value", y = "Count")
gg

Results table

Below is a table of genes that were found to be differentially expressed, ordered by their respective p-values. The 95% confidence intervals are given with the estimated LFC as well as the BH adjusted p-values and the log-odds that the gene is differentially expressed. Here we report for interest sake all genes up to a adjusted p-value threshold of 0.1.

setwd(wd)
# Load additional gene information
GeneAnnotationPlasmoDB <- fread("./data/GeneAnnotationPlasmoDB.txt", data.table = FALSE, na.strings = "N/A")

# First lets import some additional gene information to make a nicer table
GeneAnnotationPlasmoDB <- GeneAnnotationPlasmoDB[, colnames(GeneAnnotationPlasmoDB) %in% c("[Gene ID]", "[Product Description]", "[Gene Name or Symbol]")]
top_ring_ruv <- merge(top_ring_ruv, GeneAnnotationPlasmoDB, by.x = 0, by.y = "[Gene ID]", all.x = TRUE)
top_ring_ruv <- top_ring_ruv[with(top_ring_ruv, order(adj.P.Val)), ]

# Now print the table
top_ring_ruv$P.Value <- format(top_ring_ruv$P.Value, scientific = TRUE, digits = 3)
top_ring_ruv$adj.P.Val <- format(top_ring_ruv$adj.P.Val, scientific = TRUE, digits = 3)
kable(top_ring_ruv[, c(2:4, 6:ncol(top_ring_ruv))], digits = 3)
GeneID Chr Start Strand Length logFC CI.L CI.R AveExpr t P.Value adj.P.Val B [Product Description] [Gene Name or Symbol]
15 PF3D7_0202000 Pf3D7_02_v3 103385 - 2412 -2.278 -2.637 -1.918 14.110 -6.254 3.21e-07 1.33e-03 6.653 knob-associated histidine-rich protein KAHRP
55 PF3D7_0400100 Pf3D7_04_v3 28706 + 8972 -1.593 -2.375 -0.811 4.842 -5.412 3.06e-06 6.35e-03 4.487 erythrocyte membrane protein 1, PfEMP1 VAR
11 PF3D7_0115700 Pf3D7_01_v3 607390 - 7504 -1.460 -2.203 -0.718 4.616 -4.768 2.42e-05 9.51e-03 2.581 erythrocyte membrane protein 1, PfEMP1 VAR
43 PF3D7_0316600 Pf3D7_03_v3 669302 - 1572 -1.586 -1.920 -1.251 10.261 -5.022 1.30e-05 9.51e-03 3.090 formate-nitrite transporter FNT
132 PF3D7_0532400 Pf3D7_05_v3 1312471 + 1684 -1.578 -2.148 -1.008 8.158 -4.801 2.53e-05 9.51e-03 2.485 lysine-rich membrane-associated PHISTb protein LyMP
133 PF3D7_0600600 Pf3D7_06_v3 29618 - 1867 -1.767 -2.391 -1.143 3.001 -4.797 2.21e-05 9.51e-03 2.595 erythrocyte membrane protein 1 (PfEMP1), exon 2 VAR
156 PF3D7_0626200 Pf3D7_06_v3 1058666 - 1257 1.729 1.206 2.252 2.767 4.702 2.98e-05 9.51e-03 2.324 conserved Plasmodium protein, unknown function NA
238 PF3D7_0900100 Pf3D7_09_v3 20080 + 7806 -1.469 -1.999 -0.940 4.728 -5.062 9.47e-06 9.51e-03 3.443 erythrocyte membrane protein 1, PfEMP1 VAR
302 PF3D7_1023600 Pf3D7_10_v3 987358 - 2791 -1.830 -2.404 -1.256 -0.002 -4.772 2.39e-05 9.51e-03 2.211 conserved Plasmodium protein, unknown function NA
340 PF3D7_1123100 Pf3D7_11_v3 909366 + 6959 -0.572 -1.113 -0.031 9.128 -4.775 2.37e-05 9.51e-03 2.476 calcium-dependent protein kinase 7 CDPK7
431 PF3D7_1255200 Pf3D7_12_v3 2241271 - 7692 -1.472 -2.856 -0.088 4.501 -5.017 1.09e-05 9.51e-03 3.308 erythrocyte membrane protein 1, PfEMP1 VAR
449 PF3D7_1318300 Pf3D7_13_v3 753910 + 5523 -1.202 -1.561 -0.843 5.739 -4.824 2.03e-05 9.51e-03 2.722 conserved Plasmodium protein, unknown function NA
561 PF3D7_1451800 Pf3D7_14_v3 2123461 + 3139 -0.858 -1.551 -0.166 4.582 -4.721 2.81e-05 9.51e-03 2.439 sortilin NA
8 PF3D7_0109700 Pf3D7_01_v3 379149 - 658 -1.506 -2.567 -0.445 4.189 -4.673 3.27e-05 9.67e-03 2.297 rRNA biogenesis protein RRP36, putative RRP36
179 PF3D7_0712600 Pf3D7_07_v3 566726 - 7583 -1.776 -2.493 -1.059 3.427 -4.632 3.78e-05 9.79e-03 2.147 erythrocyte membrane protein 1, PfEMP1 VAR
255 PF3D7_0917800 Pf3D7_09_v3 734629 + 1314 1.904 1.427 2.380 1.361 4.576 4.43e-05 9.79e-03 1.862 conserved Plasmodium protein, unknown function NA
379 PF3D7_1213100 Pf3D7_12_v3 576417 - 164 -2.457 -2.730 -2.184 2.284 -4.631 3.98e-05 9.79e-03 2.014 U1 spliceosomal RNA NA
390 PF3D7_1223900 Pf3D7_12_v3 972710 - 684 -2.060 -2.353 -1.767 2.684 -4.612 4.24e-05 9.79e-03 2.051 50S ribosomal protein L24, putative NA
447 PF3D7_1316600 Pf3D7_13_v3 691014 + 3112 -1.238 -2.069 -0.406 6.487 -4.584 4.49e-05 9.79e-03 1.953 choline-phosphate cytidylyltransferase CCT
321 PF3D7_1105100 Pf3D7_11_v3 226065 + 354 -0.960 -1.671 -0.249 9.757 -4.561 4.74e-05 9.81e-03 1.814 histone H2B H2B
78 PF3D7_0419800 Pf3D7_04_v3 874811 - 711 0.716 -1.083 2.515 5.909 4.472 6.14e-05 1.11e-02 1.682 60S ribosomal protein L7ae/L30e, putative NA
110 PF3D7_0519500 Pf3D7_05_v3 801450 - 7678 -0.939 -1.829 -0.050 7.051 -4.496 5.70e-05 1.11e-02 1.702 carbon catabolite repressor protein 4, putative CCR4
232 PF3D7_0830300 Pf3D7_08_v3 1290240 - 1167 1.706 1.309 2.104 1.974 4.482 5.95e-05 1.11e-02 1.663 sporozoite invasion-associated protein 2 SIAP2
161 PF3D7_0632800 Pf3D7_06_v3 1374797 - 7831 -1.339 -1.647 -1.031 4.626 -4.427 7.06e-05 1.17e-02 1.598 erythrocyte membrane protein 1, PfEMP1 VAR
205 PF3D7_0805600 Pf3D7_08_v3 312034 + 927 0.854 0.534 1.174 7.166 4.437 6.86e-05 1.17e-02 1.517 PAP2-like protein, putative NA
9 PF3D7_0113000 Pf3D7_01_v3 487892 - 2236 -1.616 -2.626 -0.607 11.389 -4.434 8.44e-05 1.34e-02 1.297 glutamic acid-rich protein GARP
398 PF3D7_1230500 Pf3D7_12_v3 1253973 - 1509 0.991 0.394 1.587 4.457 4.358 8.75e-05 1.34e-02 1.402 WD repeat-containing protein, putative NA
307 PF3D7_1028000 Pf3D7_10_v3 1160031 + 3391 -0.965 -2.000 0.070 6.451 -4.321 9.84e-05 1.36e-02 1.207 methyltransferase, putative NA
391 PF3D7_1224000 Pf3D7_12_v3 974372 + 1170 -1.561 -1.919 -1.204 2.752 -4.337 9.34e-05 1.36e-02 1.333 GTP cyclohydrolase I GCH1
423 PF3D7_1249000 Pf3D7_12_v3 2005175 - 2019 1.054 0.057 2.051 1.209 4.320 9.87e-05 1.36e-02 1.181 conserved Plasmodium membrane protein, unknown function NA
365 PF3D7_1200100 Pf3D7_12_v3 16973 + 7525 -1.587 -2.095 -1.079 4.080 -4.313 1.03e-04 1.38e-02 1.258 erythrocyte membrane protein 1, PfEMP1 VAR
29 PF3D7_0223500 Pf3D7_02_v3 916352 - 7297 -0.985 -1.643 -0.327 5.295 -4.252 1.22e-04 1.39e-02 1.076 erythrocyte membrane protein 1, PfEMP1 VAR
177 PF3D7_0711200 Pf3D7_07_v3 495238 + 3003 1.358 0.537 2.179 2.233 4.245 1.24e-04 1.39e-02 1.042 conserved Plasmodium protein, unknown function NA
201 PF3D7_0802000 Pf3D7_08_v3 146089 + 4194 -1.481 -1.878 -1.084 9.158 -4.326 1.11e-04 1.39e-02 1.065 glutamate dehydrogenase, putative GDH3
208 PF3D7_0809100 Pf3D7_08_v3 459312 + 7256 -1.692 -2.453 -0.930 3.274 -4.264 1.19e-04 1.39e-02 1.122 erythrocyte membrane protein 1, PfEMP1 VAR
435 PF3D7_1303000 Pf3D7_13_v3 158144 + 635 -1.142 -2.019 -0.265 3.361 -4.271 1.15e-04 1.39e-02 1.162 conserved Plasmodium protein, unknown function NA
467 PF3D7_1344800 Pf3D7_13_v3 1796274 + 1436 -0.754 -1.088 -0.420 6.277 -4.260 1.19e-04 1.39e-02 1.045 aspartate carbamoyltransferase ATCase
357 PF3D7_1140200 Pf3D7_11_v3 1601257 - 1822 -1.598 -2.428 -0.767 3.868 -4.232 1.33e-04 1.45e-02 1.028 conserved Plasmodium protein, unknown function NA
6 PF3D7_0106000 Pf3D7_01_v3 255775 - 2769 1.082 -0.403 2.567 1.575 4.186 1.49e-04 1.55e-02 0.855 conserved Plasmodium protein, unknown function NA
549 PF3D7_1445600 Pf3D7_14_v3 1871778 + 2604 0.758 -0.019 1.536 8.240 4.184 1.50e-04 1.55e-02 0.739 RNA-binding protein, putative NA
163 PF3D7_0703100 Pf3D7_07_v3 121414 + 543 0.953 0.263 1.643 3.538 4.162 1.60e-04 1.61e-02 0.861 conserved Plasmodium protein, unknown function NA
565 PF3D7_1457000 Pf3D7_14_v3 2336649 - 2505 -0.729 -1.154 -0.304 8.941 -4.157 1.63e-04 1.61e-02 0.648 signal peptide peptidase SPP
131 PF3D7_0532300 Pf3D7_05_v3 1308278 + 1663 -1.393 -1.808 -0.978 10.836 -4.180 1.74e-04 1.68e-02 0.615 Plasmodium exported protein (PHISTb), unknown function NA
32 PF3D7_0302800 Pf3D7_03_v3 148046 - 1260 1.219 0.925 1.512 5.255 4.099 1.98e-04 1.82e-02 0.629 conserved Plasmodium protein, unknown function NA
353 PF3D7_1135300 Pf3D7_11_v3 1381015 - 1230 1.241 0.106 2.377 2.278 4.080 2.06e-04 1.82e-02 0.611 conserved Plasmodium membrane protein, unknown function NA
372 PF3D7_1206300 Pf3D7_12_v3 281020 - 8283 -1.582 -2.221 -0.943 1.502 -4.094 1.97e-04 1.82e-02 0.619 conserved Plasmodium protein, unknown function NA
412 PF3D7_1244200 Pf3D7_12_v3 1852844 - 2838 1.134 0.645 1.623 5.492 4.087 2.03e-04 1.82e-02 0.589 RNA polymerase II transcription factor B subunit 2, putative TFB2
129 PF3D7_0529000 Pf3D7_05_v3 1186787 - 2160 0.475 -0.143 1.092 7.634 4.064 2.17e-04 1.84e-02 0.409 conserved Plasmodium protein, unknown function NA
222 PF3D7_0822200 Pf3D7_08_v3 982570 + 5127 1.148 0.789 1.508 2.978 4.038 2.34e-04 1.84e-02 0.519 conserved Plasmodium membrane protein, unknown function NA
262 PF3D7_0925300 Pf3D7_09_v3 1019164 - 1740 1.901 1.624 2.177 0.157 4.031 2.39e-04 1.84e-02 0.362 proline–tRNA ligase, putative aPRS
332 PF3D7_1118400 Pf3D7_11_v3 699869 - 921 1.121 0.356 1.885 3.285 4.055 2.22e-04 1.84e-02 0.568 haloacid dehalogenase-like hydrolase, putative NA
396 PF3D7_1228800 Pf3D7_12_v3 1169557 - 9630 -0.548 -0.835 -0.262 6.866 -4.059 2.19e-04 1.84e-02 0.432 WD repeat-containing protein, putative NA
480 PF3D7_1354300 Pf3D7_13_v3 2164239 - 3178 -0.548 -1.100 0.004 9.446 -4.036 2.36e-04 1.84e-02 0.284 large subunit rRNA methyltransferase, putative NA
580 PF3D7_1470200 Pf3D7_14_v3 2877586 - 1163 -0.728 -1.031 -0.425 5.419 -4.044 2.30e-04 1.84e-02 0.484 conserved Plasmodium protein, unknown function NA
1 mal_rna_11:rRNA M76611 1916 - 108 -1.715 -2.483 -0.948 1.846 -3.991 2.70e-04 1.84e-02 0.352 NA NA
14 PF3D7_0201900 Pf3D7_02_v3 91318 - 7521 -1.731 -2.587 -0.876 10.606 -4.025 2.92e-04 1.84e-02 0.144 erythrocyte membrane protein 3 EMP3
28 PF3D7_0220500 Pf3D7_02_v3 823825 - 1040 -1.038 -1.822 -0.255 6.499 -3.965 2.97e-04 1.84e-02 0.181 Plasmodium exported protein (hyp2), unknown function NA
151 PF3D7_0622700 Pf3D7_06_v3 916000 - 1300 1.664 0.942 2.387 1.445 3.971 2.87e-04 1.84e-02 0.296 conserved Plasmodium membrane protein, unknown function NA
198 PF3D7_0800100 Pf3D7_08_v3 21361 + 7293 -1.635 -2.151 -1.119 4.419 -3.980 2.94e-04 1.84e-02 0.310 erythrocyte membrane protein 1, PfEMP1 VAR
378 PF3D7_1212800 Pf3D7_12_v3 565966 + 966 1.057 0.718 1.397 2.461 3.989 2.71e-04 1.84e-02 0.377 iron-sulfur subunit of succinate dehydrogenase NA
393 PF3D7_1225600 Pf3D7_12_v3 1035261 - 2895 -0.530 -1.045 -0.015 8.015 -4.000 2.63e-04 1.84e-02 0.210 conserved Plasmodium protein, unknown function NA
417 PF3D7_1246600 Pf3D7_12_v3 1936522 + 1173 -0.817 -1.610 -0.024 5.429 -3.970 2.87e-04 1.84e-02 0.271 pre-mRNA-splicing factor CWC26, putative BUD13
438 PF3D7_1305400 Pf3D7_13_v3 268785 - 1953 0.657 -0.823 2.136 5.323 4.013 2.53e-04 1.84e-02 0.394 AAR2 protein, putative NA
441 PF3D7_1307700 Pf3D7_13_v3 344525 + 3708 0.667 -0.041 1.375 6.400 4.021 2.47e-04 1.84e-02 0.350 conserved Plasmodium protein, unknown function NA
517 PF3D7_1414200 Pf3D7_14_v3 564024 - 1224 0.759 -0.314 1.832 5.905 3.959 2.97e-04 1.84e-02 0.212 conserved Plasmodium protein, unknown function NA
525 PF3D7_1421150 Pf3D7_14_v3 875173 - 149 -1.635 -2.311 -0.959 1.041 -3.963 2.93e-04 1.84e-02 0.237 C/D small nucleolar RNA NA
547 PF3D7_1444800 Pf3D7_14_v3 1844041 - 1577 -0.762 -1.476 -0.048 10.314 -3.999 2.63e-04 1.84e-02 0.184 fructose-bisphosphate aldolase FBPA
60 PF3D7_0404600 Pf3D7_04_v3 247731 + 12417 -1.517 -1.762 -1.272 7.591 -3.910 3.91e-04 2.00e-02 -0.094 conserved Plasmodium membrane protein, unknown function NA
62 PF3D7_0404900 Pf3D7_04_v3 267244 - 1137 1.762 1.387 2.137 3.392 3.926 3.41e-04 2.00e-02 0.192 6-cysteine protein P41
68 PF3D7_0412700 Pf3D7_04_v3 561667 - 7676 -1.390 -2.006 -0.774 4.815 -3.878 3.92e-04 2.00e-02 0.031 erythrocyte membrane protein 1, PfEMP1 VAR
166 PF3D7_0704600 Pf3D7_07_v3 216024 - 13049 -0.601 -0.849 -0.353 10.219 -3.887 3.68e-04 2.00e-02 -0.143 E3 ubiquitin-protein ligase UT
182 PF3D7_0713600 Pf3D7_07_v3 617933 + 2935 1.307 0.675 1.939 3.292 3.912 3.42e-04 2.00e-02 0.186 mitochondrial ribosomal protein S5 precursor, putative NA
204 PF3D7_0804900 Pf3D7_08_v3 279711 - 1476 0.931 0.413 1.449 5.943 3.898 3.57e-04 2.00e-02 0.039 GTPase-activating protein, putative NA
225 PF3D7_0823200 Pf3D7_08_v3 1022629 - 1218 -0.667 -1.309 -0.024 9.598 -3.887 3.69e-04 2.00e-02 -0.141 RNA-binding protein, putative NA
273 PF3D7_1000100 Pf3D7_10_v3 28490 + 7675 -1.293 -1.978 -0.608 4.472 -3.882 3.79e-04 2.00e-02 0.072 erythrocyte membrane protein 1, PfEMP1 VAR
314 PF3D7_1100100 Pf3D7_11_v3 24160 + 7439 -1.070 -1.527 -0.612 4.769 -3.921 3.33e-04 2.00e-02 0.174 erythrocyte membrane protein 1, PfEMP1 VAR
326 PF3D7_1108700 Pf3D7_11_v3 373238 - 1623 0.790 0.254 1.326 6.852 3.899 3.55e-04 2.00e-02 -0.012 heat shock protein DnaJ homologue Pfj2 NA
331 PF3D7_1115200 Pf3D7_11_v3 576773 + 3504 -0.688 -1.153 -0.222 8.257 -3.873 3.84e-04 2.00e-02 -0.152 histone-lysine N-methyltransferase SET7 SET7
336 PF3D7_1121100 Pf3D7_11_v3 794254 - 5308 -0.787 -1.146 -0.428 8.462 -3.879 3.78e-04 2.00e-02 -0.128 conserved Plasmodium protein, unknown function NA
448 PF3D7_1316900 Pf3D7_13_v3 701047 - 2877 0.669 0.447 0.890 7.724 3.893 3.62e-04 2.00e-02 -0.078 conserved Plasmodium protein, unknown function NA
470 PF3D7_1346200 Pf3D7_13_v3 1845878 - 507 2.097 1.692 2.503 0.972 3.900 3.62e-04 2.00e-02 0.074 nuclear import protein MOG1, putative NA
84 PF3D7_0500100 Pf3D7_05_v3 20929 + 7528 -1.296 -1.730 -0.862 3.384 -3.852 4.10e-04 2.01e-02 0.026 erythrocyte membrane protein 1, PfEMP1 VAR
147 PF3D7_0617200 Pf3D7_06_v3 717050 + 1868 -1.075 -1.588 -0.563 7.942 -3.873 4.08e-04 2.01e-02 -0.187 conserved Plasmodium protein, unknown function NA
226 PF3D7_0823800 Pf3D7_08_v3 1043813 + 1968 -0.846 -1.237 -0.454 5.211 -3.848 4.14e-04 2.01e-02 -0.075 DnaJ protein, putative NA
343 PF3D7_1126300 Pf3D7_11_v3 1026976 + 2569 1.116 0.621 1.612 4.598 3.845 4.18e-04 2.01e-02 -0.032 DnaJ protein, putative NA
394 PF3D7_1226600 Pf3D7_12_v3 1077868 - 909 1.632 0.899 2.365 -0.314 3.852 4.09e-04 2.01e-02 -0.109 proliferating cell nuclear antigen 2 PCNA2
389 PF3D7_1223400 Pf3D7_12_v3 941125 + 5621 -0.716 -1.080 -0.353 11.240 -3.839 4.26e-04 2.03e-02 -0.277 phospholipid-transporting ATPase, putative NA
173 PF3D7_0708500 Pf3D7_07_v3 385583 - 2739 -0.777 -1.070 -0.484 6.710 -3.831 4.35e-04 2.03e-02 -0.202 heat shock protein 86 family protein NA
492 PF3D7_1365600 Pf3D7_13_v3 2621261 + 2740 0.751 0.214 1.288 4.165 3.835 4.31e-04 2.03e-02 -0.034 DNA topoisomerase VI, b subunit, putative NA
13 PF3D7_0201800 Pf3D7_02_v3 86832 - 1960 -0.631 -1.267 0.004 9.431 -3.809 4.65e-04 2.05e-02 -0.356 knob associated heat shock protein 40 KAHsp40
98 PF3D7_0512000 Pf3D7_05_v3 527639 + 1028 -1.003 -1.949 -0.057 5.293 -3.812 4.61e-04 2.05e-02 -0.163 prefoldin subunit 6, putative NA
277 PF3D7_1003900 Pf3D7_10_v3 177921 + 950 1.720 0.913 2.527 0.292 3.815 4.58e-04 2.05e-02 -0.161 conserved Plasmodium protein, unknown function NA
281 PF3D7_1009300 Pf3D7_10_v3 377906 - 1803 1.321 0.834 1.808 3.025 3.811 4.63e-04 2.05e-02 -0.082 conserved Plasmodium protein, unknown function NA
291 PF3D7_1016100 Pf3D7_10_v3 643558 - 774 1.267 0.935 1.599 0.676 3.817 4.55e-04 2.05e-02 -0.137 conserved Plasmodium protein, unknown function NA
93 PF3D7_0509000 Pf3D7_05_v3 376855 - 1598 -0.556 -2.114 1.002 5.821 -3.788 4.96e-04 2.14e-02 -0.267 SNAP protein (soluble N-ethylmaleimide-sensitive factor attachment protein), putative NA
432 PF3D7_1301400 Pf3D7_13_v3 82718 + 1301 -1.218 -2.217 -0.219 8.056 -3.813 4.95e-04 2.14e-02 -0.337 Plasmodium exported protein (hyp12), unknown function HYP12
22 PF3D7_0209700 Pf3D7_02_v3 400153 - 1707 0.605 -0.707 1.917 8.782 3.780 5.07e-04 2.17e-02 -0.427 RING zinc finger protein, putative NA
45 PF3D7_0317500 Pf3D7_03_v3 716523 - 5309 0.696 0.032 1.361 7.107 3.771 5.20e-04 2.19e-02 -0.390 kinesin-5 EG5
220 PF3D7_0821500 Pf3D7_08_v3 967901 - 840 0.850 0.612 1.088 4.882 3.763 5.33e-04 2.19e-02 -0.262 ribosomal RNA small subunit methyltransferase NEP1, putative NEP1
333 PF3D7_1119200 Pf3D7_11_v3 722717 - 573 -1.138 -2.235 -0.040 3.872 -3.769 5.24e-04 2.19e-02 -0.200 conserved protein, unknown function NA
482 PF3D7_1355700 Pf3D7_13_v3 2206592 - 3867 1.310 0.512 2.109 7.281 3.793 5.34e-04 2.19e-02 -0.399 NLI interacting factor-like phosphatase, putative NIF3
500 PF3D7_1401400 Pf3D7_14_v3 53411 - 324 -0.820 -1.224 -0.416 12.486 -3.765 5.38e-04 2.19e-02 -0.485 early transcribed membrane protein 14.1 ETRAMP14
130 PF3D7_0531000 Pf3D7_05_v3 1267410 + 2130 0.770 0.513 1.027 5.006 3.744 5.64e-04 2.27e-02 -0.321 conserved Plasmodium protein, unknown function NA
341 PF3D7_1124800 Pf3D7_11_v3 976880 - 1057 -0.601 -0.891 -0.311 6.706 -3.738 5.74e-04 2.29e-02 -0.458 nuclear preribosomal assembly protein, putative NA
77 PF3D7_0419500 Pf3D7_04_v3 866501 - 1611 1.278 -0.047 2.603 3.860 3.728 5.91e-04 2.29e-02 -0.312 conserved Plasmodium membrane protein, unknown function NA
187 PF3D7_0717600 Pf3D7_07_v3 758720 - 4158 -1.552 -1.881 -1.222 3.062 -3.737 5.89e-04 2.29e-02 -0.295 conserved Plasmodium protein, unknown function NA
272 PF3D7_0936800 Pf3D7_09_v3 1458392 + 1471 -1.129 -1.403 -0.854 10.817 -3.758 5.84e-04 2.29e-02 -0.546 Plasmodium exported protein (PHISTc), unknown function NA
92 PF3D7_0508700 Pf3D7_05_v3 358261 + 4473 -0.502 -1.380 0.376 7.632 -3.707 6.29e-04 2.34e-02 -0.595 pre-mRNA-processing ATP-dependent RNA helicase PRP5, putative PRP5
159 PF3D7_0629600 Pf3D7_06_v3 1218307 + 945 0.513 0.284 0.742 4.955 3.711 6.21e-04 2.34e-02 -0.409 conserved Plasmodium protein, unknown function NA
297 PF3D7_1019100 Pf3D7_10_v3 766168 - 5787 -1.541 -1.883 -1.198 0.833 -3.705 6.33e-04 2.34e-02 -0.392 conserved Plasmodium protein, unknown function NA
317 PF3D7_1102800 Pf3D7_11_v3 131703 - 285 -0.917 -1.176 -0.657 13.477 -3.727 6.12e-04 2.34e-02 -0.593 early transcribed membrane protein 11.2 ETRAMP11.2
361 PF3D7_1145500 Pf3D7_11_v3 1807359 + 2772 1.127 0.388 1.866 1.570 3.708 6.28e-04 2.34e-02 -0.364 ABC transporter B family member 3, putative ABCB3
240 PF3D7_0903200 Pf3D7_09_v3 133762 - 1826 -0.871 -1.268 -0.475 5.122 -3.701 6.40e-04 2.35e-02 -0.460 ras-related protein RAB7 RAB7
264 PF3D7_0928500 Pf3D7_09_v3 1146239 - 959 -1.140 -2.966 0.686 2.706 -3.698 6.46e-04 2.35e-02 -0.375 conserved Plasmodium protein, unknown function NA
408 PF3D7_1240900 Pf3D7_12_v3 1735543 + 7866 -1.353 -1.614 -1.092 4.223 -3.693 6.65e-04 2.40e-02 -0.422 erythrocyte membrane protein 1, PfEMP1 VAR
137 PF3D7_0606800 Pf3D7_06_v3 288377 - 900 1.561 0.769 2.354 3.353 3.686 6.84e-04 2.40e-02 -0.426 probable protein, unknown function NA
466 PF3D7_1344200 Pf3D7_13_v3 1769129 + 2799 -0.566 -1.078 -0.055 9.450 -3.679 6.83e-04 2.40e-02 -0.720 heat shock protein 110, putative HSP110
552 PF3D7_1446900 Pf3D7_14_v3 1924425 - 2226 0.742 0.467 1.017 6.855 3.679 6.83e-04 2.40e-02 -0.624 glutaminyl-peptide cyclotransferase, putative NA
235 PF3D7_0831700 Pf3D7_08_v3 1365467 - 2040 -0.882 -1.398 -0.366 13.476 -3.683 6.92e-04 2.41e-02 -0.708 heat shock protein 70 HSP70-x
165 PF3D7_0703400 Pf3D7_07_v3 129370 - 2463 1.213 0.733 1.693 3.356 3.663 7.15e-04 2.47e-02 -0.470 conserved Plasmodium protein, unknown function NA
582 PF3D7_1472300 Pf3D7_14_v3 2954108 + 3001 1.117 0.747 1.486 4.456 3.650 7.44e-04 2.55e-02 -0.544 conserved Plasmodium membrane protein, unknown function NA
180 PF3D7_0712800 Pf3D7_07_v3 581386 - 7538 -1.220 -1.762 -0.678 4.050 -3.644 7.56e-04 2.55e-02 -0.534 erythrocyte membrane protein 1, PfEMP1 VAR
322 PF3D7_1105300 Pf3D7_11_v3 231847 - 2392 1.349 0.827 1.871 1.730 3.646 7.51e-04 2.55e-02 -0.515 conserved Plasmodium protein, unknown function NA
533 PF3D7_1428100 Pf3D7_14_v3 1098038 - 1914 0.940 0.663 1.217 3.882 3.633 7.82e-04 2.61e-02 -0.565 WW domain-binding protein 11, putative NA
292 PF3D7_1016200 Pf3D7_10_v3 646054 + 1683 1.116 0.713 1.519 4.605 3.619 8.13e-04 2.70e-02 -0.636 Rab3 GTPase-activating protein non-catalytic subunit, putative NA
63 PF3D7_0405400 Pf3D7_04_v3 291251 + 9726 -0.560 -1.202 0.081 10.721 -3.607 8.43e-04 2.71e-02 -0.921 pre-mRNA-processing-splicing factor 8, putative PRPF8
194 PF3D7_0723900 Pf3D7_07_v3 1000701 - 4046 -0.617 -1.753 0.519 7.841 -3.606 8.45e-04 2.71e-02 -0.878 RNA-binding protein, putative NA
445 PF3D7_1309600 Pf3D7_13_v3 438510 + 867 0.851 0.427 1.276 4.331 3.613 8.28e-04 2.71e-02 -0.632 ribosomal RNA methyltransferase, putative NA
452 PF3D7_1321700 Pf3D7_13_v3 902383 + 2784 -0.549 -1.144 0.046 9.143 -3.606 8.44e-04 2.71e-02 -0.915 splicing factor 1 SF1
303 PF3D7_1025000 Pf3D7_10_v3 1045608 - 4153 -0.567 -1.130 -0.005 8.288 -3.596 8.69e-04 2.75e-02 -0.912 formin 2, putative NA
512 PF3D7_1410500 Pf3D7_14_v3 423751 - 500 1.138 0.408 1.869 1.432 3.596 8.71e-04 2.75e-02 -0.649 conserved Plasmodium protein, unknown function NA
489 PF3D7_1364000 Pf3D7_13_v3 2564625 + 2484 1.063 0.739 1.388 3.834 3.586 8.95e-04 2.81e-02 -0.680 conserved Plasmodium protein, unknown function NA
443 PF3D7_1309100 Pf3D7_13_v3 418820 + 1302 -0.800 -1.672 0.073 8.874 -3.580 9.25e-04 2.88e-02 -0.995 60S ribosomal protein L24, putative NA
100 PF3D7_0513600 Pf3D7_05_v3 574941 - 3565 -0.958 -2.280 0.365 5.653 -3.563 9.64e-04 2.96e-02 -0.872 deoxyribodipyrimidine photo-lyase, putative NA
433 PF3D7_1302700 Pf3D7_13_v3 145174 + 5025 -0.478 -1.596 0.641 8.872 -3.562 9.60e-04 2.96e-02 -1.031 ATP-dependent RNA helicase DHR1, putative NA
382 PF3D7_1215900 Pf3D7_12_v3 641552 + 1968 0.843 0.572 1.113 4.860 3.553 9.86e-04 3.00e-02 -0.822 serpentine receptor, putative SR10
12 PF3D7_0201600 Pf3D7_02_v3 77251 - 1558 -0.800 -1.061 -0.538 9.183 -3.546 1.02e-03 3.01e-02 -1.077 PHISTb domain-containing RESA-like protein 1 RLP1
25 PF3D7_0218700 Pf3D7_02_v3 763491 - 1701 -0.710 -1.254 -0.167 7.132 -3.547 1.00e-03 3.01e-02 -1.000 pre-mRNA-processing protein 45, putative PRP45
72 PF3D7_0416100 Pf3D7_04_v3 706529 + 2481 -1.006 -1.674 -0.337 4.181 -3.533 1.05e-03 3.01e-02 -0.855 glutamyl-tRNA(Gln) amidotransferase subunit A GATA
150 PF3D7_0621500 Pf3D7_06_v3 881963 + 1032 1.105 0.673 1.537 1.210 3.537 1.03e-03 3.01e-02 -0.795 ribonuclease P/MRP protein subunit RPP1, putative RPP1
374 PF3D7_1208600 Pf3D7_12_v3 402300 + 228 -0.766 -1.004 -0.528 3.774 -3.537 1.03e-03 3.01e-02 -0.819 mitochondrial import inner membrane translocase subunit TIM10, putative TIM10
541 PF3D7_1437800 Pf3D7_14_v3 1530276 - 555 1.908 1.376 2.440 2.848 3.556 1.02e-03 3.01e-02 -0.767 trafficking protein particle complex subunit 5, putative TRAPPC5
555 PF3D7_1449900 Pf3D7_14_v3 2044007 - 1023 1.254 0.706 1.803 2.664 3.544 1.01e-03 3.01e-02 -0.765 conserved Plasmodium protein, unknown function NA
567 PF3D7_1457900 Pf3D7_14_v3 2375579 + 10368 -0.647 -0.867 -0.426 5.665 -3.533 1.04e-03 3.01e-02 -0.933 conserved Plasmodium protein, unknown function NA
413 PF3D7_1244300 Pf3D7_12_v3 1857849 + 242 -1.943 -2.298 -1.587 2.556 -3.524 1.11e-03 3.18e-02 -0.840 ACEA small nucleolar RNA U3 NA
279 PF3D7_1004400 Pf3D7_10_v3 207000 - 2643 -0.851 -1.643 -0.059 5.835 -3.497 1.16e-03 3.26e-02 -1.046 RNA-binding protein, putative NA
550 PF3D7_1445800 Pf3D7_14_v3 1878658 - 3920 1.031 0.476 1.587 1.557 3.498 1.16e-03 3.26e-02 -0.883 conserved Plasmodium membrane protein, unknown function NA
568 PF3D7_1458000 Pf3D7_14_v3 2387786 + 1710 0.358 -0.401 1.117 8.181 3.495 1.16e-03 3.26e-02 -1.188 cysteine proteinase falcipain 1 FP1
213 PF3D7_0814100 Pf3D7_08_v3 682518 - 1055 0.932 0.352 1.512 4.301 3.479 1.22e-03 3.31e-02 -0.979 conserved Plasmodium protein, unknown function NA
285 PF3D7_1013000 Pf3D7_10_v3 500210 + 2012 1.069 0.789 1.349 2.762 3.484 1.20e-03 3.31e-02 -0.917 zinc finger protein, putative NA
289 PF3D7_1015600 Pf3D7_10_v3 627044 - 1997 -0.862 -1.191 -0.533 5.366 -3.477 1.23e-03 3.31e-02 -1.075 heat shock protein 60 HSP60
329 PF3D7_1111300 Pf3D7_11_v3 442959 - 870 0.861 0.490 1.232 2.957 3.479 1.22e-03 3.31e-02 -0.928 SNARE protein, putative GS27
370 PF3D7_1205700 Pf3D7_12_v3 253155 + 969 1.137 0.380 1.894 0.854 3.476 1.23e-03 3.31e-02 -0.947 targeted glyoxalase II tGloII
469 PF3D7_1345200 Pf3D7_13_v3 1812220 - 1710 0.993 -0.133 2.120 3.418 3.476 1.23e-03 3.31e-02 -0.948 rhomboid protease ROM6, putative ROM6
310 PF3D7_1035800 Pf3D7_10_v3 1420533 + 2139 -1.550 -2.352 -0.748 9.464 -3.508 1.26e-03 3.32e-02 -1.229 probable protein, unknown function M712
359 PF3D7_1142400 Pf3D7_11_v3 1702089 - 1554 0.671 0.139 1.202 5.990 3.467 1.26e-03 3.32e-02 -1.139 coproporphyrinogen-III oxidase CPO
403 PF3D7_1234500 Pf3D7_12_v3 1439896 - 1155 0.621 0.015 1.226 4.896 3.470 1.25e-03 3.32e-02 -1.040 conserved Plasmodium protein, unknown function NA
455 PF3D7_1326700 Pf3D7_13_v3 1125280 + 1629 1.449 0.663 2.236 3.645 3.474 1.26e-03 3.32e-02 -0.978 conserved Apicomplexan protein, unknown function NA
299 PF3D7_1021900 Pf3D7_10_v3 905473 - 6873 -0.918 -1.171 -0.664 6.810 -3.462 1.31e-03 3.37e-02 -1.223 PHAX domain-containing protein, putative NA
454 PF3D7_1324200 Pf3D7_13_v3 1000100 - 1783 -0.817 -1.572 -0.061 7.184 -3.458 1.31e-03 3.37e-02 -1.246 micro-fibrillar-associated protein, putative NA
518 PF3D7_1414500 Pf3D7_14_v3 578369 - 9161 -0.606 -1.509 0.297 8.009 -3.454 1.31e-03 3.37e-02 -1.297 atypical protein kinase, ABC-1 family, putative ABCk2
90 PF3D7_0506700 Pf3D7_05_v3 280886 + 2460 -0.677 -1.739 0.385 4.990 -3.449 1.33e-03 3.38e-02 -1.122 GTPase-activating protein, putative NA
347 PF3D7_1128100 Pf3D7_11_v3 1094909 - 1023 -0.696 -1.413 0.022 5.320 -3.450 1.32e-03 3.38e-02 -1.126 prefoldin subunit 5, putative NA
79 PF3D7_0420000 Pf3D7_04_v3 894612 - 10113 -0.538 -1.185 0.108 9.307 -3.442 1.36e-03 3.41e-02 -1.358 zinc finger protein, putative NA
114 PF3D7_0522300 Pf3D7_05_v3 902613 - 2232 -0.540 -1.220 0.140 6.719 -3.442 1.36e-03 3.41e-02 -1.260 S-adenosylmethionine-dependent methyltransferase, putative NA
442 PF3D7_1308300 Pf3D7_13_v3 372260 + 387 0.483 -0.022 0.988 7.931 3.438 1.37e-03 3.42e-02 -1.336 40S ribosomal protein S27 RPS27
96 PF3D7_0511000 Pf3D7_05_v3 467585 - 516 -0.570 -1.189 0.049 8.143 -3.432 1.39e-03 3.46e-02 -1.350 translationally-controlled tumor protein homolog TCTP
89 PF3D7_0503100 Pf3D7_05_v3 127064 - 1614 -1.195 -1.694 -0.696 2.285 -3.424 1.43e-03 3.47e-02 -1.059 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative IspE
160 PF3D7_0631600 Pf3D7_06_v3 1323294 + 1142 -1.495 -2.245 -0.745 2.400 -3.430 1.41e-03 3.47e-02 -1.046 exported protein family 4 EPF4
319 PF3D7_1103400 Pf3D7_11_v3 146427 + 4389 1.195 0.875 1.515 3.144 3.423 1.43e-03 3.47e-02 -1.072 FeS cluster assembly protein SufD, putative SufD
364 PF3D7_1149500 Pf3D7_11_v3 1991359 - 2660 -0.643 -1.282 -0.003 8.035 -3.424 1.43e-03 3.47e-02 -1.355 ring-infected erythrocyte surface antigen 2, pseudogene RESA2
247 PF3D7_0907900 Pf3D7_09_v3 367865 - 925 -1.510 -2.913 -0.107 3.713 -3.434 1.44e-03 3.47e-02 -1.102 peptide deformylase PDF
122 PF3D7_0524800 Pf3D7_05_v3 1021408 - 2900 0.914 0.705 1.122 3.238 3.416 1.46e-03 3.50e-02 -1.099 ubiquitin fusion degradation protein 1, putative UFD1
4 PF3D7_0101000 Pf3D7_01_v3 65817 - 1173 -2.291 -3.297 -1.284 -1.114 -3.415 1.48e-03 3.50e-02 -1.198 rifin RIF
162 PF3D7_0700100 Pf3D7_07_v3 20307 + 7777 -1.047 -1.695 -0.399 5.134 -3.416 1.47e-03 3.50e-02 -1.202 erythrocyte membrane protein 1, PfEMP1 VAR
197 PF3D7_0733000 Pf3D7_07_v3 1417588 - 8647 -0.963 -1.570 -0.355 4.915 -3.408 1.49e-03 3.51e-02 -1.201 erythrocyte membrane protein 1, PfEMP1 VAR
85 PF3D7_0501300 Pf3D7_05_v3 68930 + 1184 -0.878 -1.677 -0.078 12.513 -3.409 1.54e-03 3.60e-02 -1.464 skeleton-binding protein 1 SBP1
366 PF3D7_1200200 Pf3D7_12_v3 26321 - 1367 -1.905 -2.207 -1.603 -0.371 -3.395 1.55e-03 3.61e-02 -1.192 rifin RIF
181 PF3D7_0713500 Pf3D7_07_v3 614385 + 2865 0.993 0.415 1.570 4.315 3.384 1.60e-03 3.70e-02 -1.219 conserved Plasmodium protein, unknown function NA
36 PF3D7_0304900 Pf3D7_03_v3 231793 - 513 0.815 -0.110 1.740 5.014 3.381 1.61e-03 3.71e-02 -1.273 conserved Plasmodium protein, unknown function NA
507 PF3D7_1404900 Pf3D7_14_v3 170000 + 894 0.417 -0.160 0.993 8.339 3.377 1.63e-03 3.73e-02 -1.509 conserved Plasmodium protein, unknown function NA
81 PF3D7_0423800 Pf3D7_04_v3 1076347 + 1188 1.880 1.141 2.620 2.150 3.388 1.64e-03 3.73e-02 -1.171 cysteine-rich protective antigen CyRPA
271 PF3D7_0935900 Pf3D7_09_v3 1420483 - 2325 -0.731 -1.228 -0.234 13.774 -3.374 1.66e-03 3.74e-02 -1.525 ring-exported protein 1 REX1
437 PF3D7_1304300 Pf3D7_13_v3 231083 + 642 1.450 1.125 1.775 0.470 3.370 1.66e-03 3.74e-02 -1.206 conserved Plasmodium protein, unknown function NA
539 PF3D7_1436500 Pf3D7_14_v3 1488706 + 1296 1.168 0.522 1.814 0.239 3.368 1.67e-03 3.74e-02 -1.221 GTP-binding protein, putative NA
311 PF3D7_1037100 Pf3D7_10_v3 1469990 - 2238 -0.903 -1.216 -0.591 3.447 -3.364 1.69e-03 3.77e-02 -1.259 pyruvate kinase 2 PyKII
451 PF3D7_1321600 Pf3D7_13_v3 897716 + 3329 1.222 0.430 2.014 0.168 3.360 1.71e-03 3.79e-02 -1.239 phosphodiesterase gamma, putative PDEgamma
16 PF3D7_0202400 Pf3D7_02_v3 120524 + 3579 -1.206 -1.524 -0.888 4.276 -3.344 1.81e-03 3.86e-02 -1.339 gamete antigen 27/25, putative NA
74 PF3D7_0417400 Pf3D7_04_v3 756294 + 20310 -0.713 -1.449 0.023 8.087 -3.340 1.82e-03 3.86e-02 -1.599 conserved Plasmodium protein, unknown function NA
141 PF3D7_0609700 Pf3D7_06_v3 413652 + 6130 -0.601 -0.938 -0.263 9.580 -3.340 1.81e-03 3.86e-02 -1.625 conserved Plasmodium protein, unknown function NA
183 PF3D7_0714600 Pf3D7_07_v3 667985 + 1728 -0.631 -1.087 -0.175 6.973 -3.344 1.79e-03 3.86e-02 -1.529 conserved Plasmodium protein, unknown function NA
268 PF3D7_0932900 Pf3D7_09_v3 1309467 - 477 0.916 0.639 1.193 2.111 3.346 1.78e-03 3.86e-02 -1.246 conserved Plasmodium protein, unknown function NA
323 PF3D7_1106300 Pf3D7_11_v3 263604 - 2967 -1.016 -1.287 -0.745 4.205 -3.344 1.79e-03 3.86e-02 -1.351 exonuclease, putative NA
404 PF3D7_1235300 Pf3D7_12_v3 1470713 + 4989 -0.615 -1.360 0.131 9.308 -3.345 1.78e-03 3.86e-02 -1.612 CCR4-NOT transcription complex subunit 4, putative NOT4
488 PF3D7_1362300 Pf3D7_13_v3 2493143 + 570 0.821 0.583 1.059 3.690 3.345 1.78e-03 3.86e-02 -1.286 conserved protein, unknown function NA
167 PF3D7_0705600 Pf3D7_07_v3 281035 - 3399 0.942 0.430 1.454 4.013 3.337 1.83e-03 3.86e-02 -1.317 RNA helicase, putative NA
246 PF3D7_0907700 Pf3D7_09_v3 364069 - 840 0.428 -1.470 2.326 7.924 3.334 1.84e-03 3.87e-02 -1.609 subunit of proteaseome activator complex, putative PA28
584 PF3D7_1474500 Pf3D7_14_v3 3055715 - 2106 0.645 0.215 1.076 6.705 3.332 1.85e-03 3.87e-02 -1.546 splicing factor 3A subunit 1, putative SF3A1
499 PF3D7_1400100 Pf3D7_14_v3 1393 + 3951 -1.493 -1.875 -1.110 4.800 -3.348 1.87e-03 3.89e-02 -1.384 erythrocyte membrane protein 1 (PfEMP1), pseudogene NA
18 PF3D7_0205400 Pf3D7_02_v3 223478 + 1374 0.422 -0.097 0.941 6.151 3.315 1.94e-03 3.98e-02 -1.545 PCI domain-containing protein, putative NA
86 PF3D7_0501400 Pf3D7_05_v3 74509 + 5334 -1.103 -2.383 0.176 11.055 -3.342 1.93e-03 3.98e-02 -1.668 interspersed repeat antigen FIRA
145 PF3D7_0614200 Pf3D7_06_v3 593172 - 2733 0.977 0.171 1.784 3.935 3.317 1.93e-03 3.98e-02 -1.364 cytosolic Fe-S cluster assembly factor NAR1, putative NAR1
453 PF3D7_1322100 Pf3D7_13_v3 920971 + 8479 -0.565 -1.024 -0.106 9.373 -3.302 2.01e-03 4.09e-02 -1.718 histone-lysine N-methyltransferase SET2 SET2
493 PF3D7_1366000 Pf3D7_13_v3 2635213 + 276 1.199 0.915 1.482 2.200 3.300 2.02e-03 4.09e-02 -1.356 conserved Plasmodium protein, unknown function NA
506 PF3D7_1404700 Pf3D7_14_v3 161227 - 873 1.202 0.598 1.806 1.784 3.300 2.02e-03 4.09e-02 -1.353 conserved Plasmodium protein, unknown function NA
170 PF3D7_0707900 Pf3D7_07_v3 366929 + 780 -0.462 -1.432 0.507 7.539 -3.297 2.04e-03 4.09e-02 -1.686 ribosomal protein S8e, putative NA
234 PF3D7_0831400 Pf3D7_08_v3 1344405 - 1083 -1.175 -1.535 -0.815 3.211 -3.300 2.04e-03 4.09e-02 -1.425 Plasmodium exported protein, unknown function NA
411 PF3D7_1244100 Pf3D7_12_v3 1847677 + 4480 -0.527 -1.212 0.158 5.926 -3.294 2.06e-03 4.10e-02 -1.589 N-alpha-acetyltransferase 15, NatA auxiliary subunit, putative NA
52 PF3D7_0323000 Pf3D7_03_v3 968675 - 528 -0.921 -1.365 -0.477 4.328 -3.289 2.09e-03 4.12e-02 -1.490 translation machinery-associated protein 7, putative TMA7
106 PF3D7_0518300 Pf3D7_05_v3 759831 - 1168 -0.466 -1.340 0.407 6.608 -3.289 2.09e-03 4.12e-02 -1.653 proteasome subunit beta type-1, putative NA
7 PF3D7_0108500 Pf3D7_01_v3 349170 + 540 -0.889 -2.271 0.492 10.229 -3.295 2.13e-03 4.17e-02 -1.766 conserved Plasmodium protein, unknown function NA
528 PF3D7_1424500 Pf3D7_14_v3 979464 + 142 -0.859 -1.122 -0.596 3.564 -3.280 2.14e-03 4.17e-02 -1.432 small nucleolar RNA snoR27 NA
557 PF3D7_1450300 Pf3D7_14_v3 2056641 + 2598 0.854 0.553 1.154 5.203 3.280 2.14e-03 4.17e-02 -1.564 NADPH–cytochrome P450 reductase, putative CPR
551 PF3D7_1446300 Pf3D7_14_v3 1898351 + 3576 1.201 0.852 1.550 4.099 3.281 2.16e-03 4.19e-02 -1.484 conserved Plasmodium membrane protein, unknown function NA
260 PF3D7_0923100 Pf3D7_09_v3 941830 - 669 1.038 0.081 1.995 1.285 3.274 2.18e-03 4.19e-02 -1.416 OTU domain-containing protein, putative NA
184 PF3D7_0716000 Pf3D7_07_v3 703207 + 3378 -0.470 -1.219 0.279 8.598 -3.270 2.20e-03 4.21e-02 -1.798 RNA-binding protein, putative NA
427 PF3D7_1251400 Pf3D7_12_v3 2097436 - 1410 1.030 0.435 1.624 1.677 3.269 2.21e-03 4.21e-02 -1.426 conserved Plasmodium protein, unknown function NA
554 PF3D7_1447200 Pf3D7_14_v3 1933985 + 1791 -0.466 -1.058 0.127 7.823 -3.262 2.25e-03 4.28e-02 -1.791 conserved Plasmodium protein, unknown function NA
402 PF3D7_1233100 Pf3D7_12_v3 1359169 + 408 -0.816 -1.368 -0.264 4.139 -3.251 2.32e-03 4.33e-02 -1.536 conserved protein, unknown function NA
532 PF3D7_1427200 Pf3D7_14_v3 1061805 + 975 -1.510 -1.777 -1.242 1.616 -3.254 2.32e-03 4.33e-02 -1.470 selenoprotein Sel4
544 PF3D7_1440200 Pf3D7_14_v3 1639477 + 7691 -0.893 -1.631 -0.155 1.898 -3.256 2.29e-03 4.33e-02 -1.464 stromal-processing peptidase, putative SPP
586 PF3D7_1476200 Pf3D7_14_v3 3133951 + 1701 -1.328 -1.802 -0.855 6.583 -3.275 2.32e-03 4.33e-02 -1.685 Plasmodium exported protein (PHISTb), unknown function NA
248 PF3D7_0909600 Pf3D7_09_v3 433238 - 2136 1.309 0.280 2.338 0.859 3.247 2.34e-03 4.36e-02 -1.483 conserved Plasmodium protein, unknown function NA
231 PF3D7_0829100 Pf3D7_08_v3 1252349 + 1448 -0.507 -1.092 0.079 7.094 -3.237 2.41e-03 4.46e-02 -1.817 conserved protein, unknown function NA
103 PF3D7_0517100 Pf3D7_05_v3 718425 - 1431 1.003 0.547 1.459 3.663 3.233 2.44e-03 4.47e-02 -1.555 conserved Plasmodium protein, unknown function NA
283 PF3D7_1011800 Pf3D7_10_v3 455398 + 3420 -0.582 -1.221 0.058 10.650 -3.234 2.43e-03 4.47e-02 -1.910 PRE-binding protein PREBP
19 PF3D7_0208200 Pf3D7_02_v3 335679 - 903 -0.382 -0.905 0.140 7.526 -3.227 2.48e-03 4.51e-02 -1.866 KRR1 small subunit processome component, putative KRR1
136 PF3D7_0605100 Pf3D7_06_v3 217240 + 2268 0.892 0.414 1.370 6.752 3.231 2.50e-03 4.51e-02 -1.816 RNA-binding protein, putative NA
400 PF3D7_1231600 Pf3D7_12_v3 1301098 - 3507 -0.662 -1.473 0.148 6.353 -3.224 2.50e-03 4.51e-02 -1.800 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2, putative PRP2
479 PF3D7_1353500 Pf3D7_13_v3 2144125 + 981 0.792 0.198 1.385 3.058 3.228 2.48e-03 4.51e-02 -1.552 RNA polymerase II transcription factor B subunit 4, putative TFB4
578 PF3D7_1468100 Pf3D7_14_v3 2786308 - 8016 -0.518 -1.168 0.132 10.232 -3.221 2.52e-03 4.53e-02 -1.941 conserved Plasmodium protein, unknown function NA
46 PF3D7_0317900 Pf3D7_03_v3 739428 + 2306 0.832 0.540 1.124 2.115 3.209 2.61e-03 4.61e-02 -1.571 conserved Plasmodium protein, unknown function NA
188 PF3D7_0719500 Pf3D7_07_v3 854652 - 2003 0.901 0.216 1.586 1.522 3.208 2.61e-03 4.61e-02 -1.569 LEM3/CDC50 family protein, putative NA
254 PF3D7_0915500 Pf3D7_09_v3 657418 + 1995 1.209 0.535 1.884 0.043 3.211 2.59e-03 4.61e-02 -1.579 conserved Plasmodium protein, unknown function NA
566 PF3D7_1457100 Pf3D7_14_v3 2340784 + 2244 -1.001 -1.317 -0.685 6.569 -3.223 2.59e-03 4.61e-02 -1.819 conserved Plasmodium protein, unknown function NA
355 PF3D7_1137300 Pf3D7_11_v3 1466197 - 2070 0.417 0.046 0.787 7.338 3.205 2.63e-03 4.62e-02 -1.909 CLPTM1 domain-containing protein, putative NA
112 PF3D7_0521000 Pf3D7_05_v3 859373 - 1691 -0.642 -1.091 -0.193 6.047 -3.202 2.66e-03 4.62e-02 -1.821 conserved Plasmodium protein, unknown function NA
126 PF3D7_0528100 Pf3D7_05_v3 1157840 - 3714 -0.403 -1.040 0.233 9.336 -3.204 2.65e-03 4.62e-02 -1.981 AP-1 complex subunit beta, putative NA
529 PF3D7_1426000 Pf3D7_14_v3 1016133 - 486 0.507 -0.016 1.030 8.634 3.198 2.69e-03 4.66e-02 -1.980 60S ribosomal protein L21 RPL21
88 PF3D7_0502500 Pf3D7_05_v3 114149 + 1785 1.651 0.516 2.786 0.248 3.195 2.71e-03 4.67e-02 -1.609 conserved Plasmodium protein, unknown function NA
169 PF3D7_0707800 Pf3D7_07_v3 362005 + 3775 0.725 0.305 1.145 2.258 3.191 2.74e-03 4.67e-02 -1.614 RAP protein, putative NA
176 PF3D7_0709600 Pf3D7_07_v3 429857 - 3902 -0.469 -1.245 0.307 7.336 -3.192 2.73e-03 4.67e-02 -1.943 ribonucleases P/MRP protein subunit POP1, putative POP1
494 PF3D7_1366500 Pf3D7_13_v3 2661573 + 450 1.113 0.527 1.698 0.692 3.194 2.72e-03 4.67e-02 -1.606 nucleoside diphosphate kinase NDK
380 PF3D7_1214300 Pf3D7_12_v3 608542 - 1472 0.720 0.483 0.958 3.646 3.185 2.79e-03 4.73e-02 -1.676 geranylgeranyl transferase type2 beta subunit, putative NA
436 PF3D7_1303100 Pf3D7_13_v3 159024 + 892 -0.803 -2.210 0.604 3.666 -3.183 2.80e-03 4.74e-02 -1.711 methyltransferase-like protein, putative NA
30 PF3D7_0300100 Pf3D7_03_v3 36965 + 7518 -0.916 -1.729 -0.104 4.393 -3.180 2.83e-03 4.76e-02 -1.739 erythrocyte membrane protein 1, PfEMP1 VAR
2 mal_rna_17:rRNA M76611 5577 - 195 -1.367 -1.613 -1.121 4.213 -3.186 2.84e-03 4.77e-02 -1.707 NA NA
351 PF3D7_1133700 Pf3D7_11_v3 1302173 + 3815 -0.628 -0.975 -0.282 10.101 -3.173 2.88e-03 4.77e-02 -2.061 FHA domain-containing protein, putative NA
352 PF3D7_1134800 Pf3D7_11_v3 1367186 + 1624 0.455 -0.083 0.993 6.513 3.172 2.89e-03 4.77e-02 -1.940 coatomer subunit delta NA
484 PF3D7_1359100 Pf3D7_13_v3 2347863 - 2124 0.651 0.215 1.087 4.613 3.172 2.89e-03 4.77e-02 -1.776 riboflavin kinase / FAD synthase family protein, putative NA
526 PF3D7_1421600 Pf3D7_14_v3 885211 + 2660 0.487 -0.563 1.537 5.100 3.175 2.86e-03 4.77e-02 -1.811 conserved Plasmodium protein, unknown function NA
536 PF3D7_1434300 Pf3D7_14_v3 1372903 + 1695 -0.405 -0.857 0.047 8.758 -3.168 2.92e-03 4.80e-02 -2.063 Hsp70/Hsp90 organizing protein HOP
118 PF3D7_0523700 Pf3D7_05_v3 980754 - 4601 1.400 1.030 1.771 0.959 3.166 2.93e-03 4.80e-02 -1.665 conserved Plasmodium membrane protein, unknown function NA
305 PF3D7_1027300 Pf3D7_10_v3 1140589 - 2014 -0.778 -1.652 0.097 8.553 -3.169 2.96e-03 4.83e-02 -2.054 peroxiredoxin nPrx
39 PF3D7_0310800 Pf3D7_03_v3 464662 + 330 0.432 -0.360 1.224 6.118 3.148 3.08e-03 4.83e-02 -1.965 conserved Plasmodium protein, unknown function NA
44 PF3D7_0317100 Pf3D7_03_v3 686282 + 3201 0.881 0.224 1.538 2.554 3.153 3.04e-03 4.83e-02 -1.711 6-cysteine protein B9
125 PF3D7_0528000 Pf3D7_05_v3 1156205 - 375 0.842 0.497 1.187 3.660 3.148 3.09e-03 4.83e-02 -1.767 proteasome maturation factor UMP1, putative UMP1
221 PF3D7_0821600 Pf3D7_08_v3 969690 + 2025 0.546 0.255 0.836 6.666 3.160 2.98e-03 4.83e-02 -1.983 clp1-related protein, putative NA
267 PF3D7_0931400 Pf3D7_09_v3 1263347 + 1484 -0.833 -1.433 -0.232 3.619 -3.147 3.09e-03 4.83e-02 -1.764 conserved Plasmodium protein, unknown function NA
316 PF3D7_1102700 Pf3D7_11_v3 128789 + 276 -0.581 -0.941 -0.221 10.495 -3.158 3.00e-03 4.83e-02 -2.103 early transcribed membrane protein 11.1 ETRAMP11.1
328 PF3D7_1111000 Pf3D7_11_v3 434802 + 1740 0.567 -0.232 1.365 5.346 3.155 3.03e-03 4.83e-02 -1.879 tRNA m5C-methyltransferase, putative NA
420 PF3D7_1247900 Pf3D7_12_v3 1972438 + 639 -0.619 -1.165 -0.073 6.344 -3.158 3.00e-03 4.83e-02 -1.955 nucleolar rRNA processing protein, putative NA
446 PF3D7_1315800 Pf3D7_13_v3 660018 - 1245 0.590 0.115 1.066 5.323 3.152 3.05e-03 4.83e-02 -1.879 transcription factor MYB1 MYB1
481 PF3D7_1355200 Pf3D7_13_v3 2191058 - 3054 1.714 1.217 2.211 0.476 3.158 3.02e-03 4.83e-02 -1.693 RAP protein, putative NA
485 PF3D7_1360100 Pf3D7_13_v3 2405249 - 969 -0.542 -1.093 0.009 5.548 -3.149 3.07e-03 4.83e-02 -1.907 RNA-binding protein, putative NA
76 PF3D7_0418300 Pf3D7_04_v3 819362 - 2979 0.592 -0.214 1.398 10.491 3.142 3.13e-03 4.88e-02 -2.141 conserved Plasmodium protein, unknown function NA
66 PF3D7_0409900 Pf3D7_04_v3 461991 - 1967 0.910 0.534 1.286 2.782 3.138 3.17e-03 4.91e-02 -1.752 actin-like protein, putative ALP5b
440 PF3D7_1306700 Pf3D7_13_v3 318332 - 1404 1.059 0.686 1.433 0.096 3.137 3.18e-03 4.92e-02 -1.744 conserved Plasmodium protein, unknown function NA
164 PF3D7_0703200 Pf3D7_07_v3 122513 - 4623 -0.952 -1.551 -0.353 4.482 -3.133 3.21e-03 4.94e-02 -1.873 conserved Plasmodium protein, unknown function NA
308 PF3D7_1030100 Pf3D7_10_v3 1224519 - 4574 -0.400 -0.931 0.130 8.748 -3.130 3.24e-03 4.98e-02 -2.159 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22, putative PRP22
358 PF3D7_1140800 Pf3D7_11_v3 1633920 + 2412 0.466 -0.235 1.166 6.642 3.127 3.27e-03 5.00e-02 -2.059 conserved Plasmodium protein, unknown function NA
542 PF3D7_1438500 Pf3D7_14_v3 1557527 - 2631 0.561 0.255 0.868 6.161 3.124 3.29e-03 5.01e-02 -2.028 cleavage and polyadenylation specificity factor subunit 3, putative CPSF3
54 PF3D7_0324900 Pf3D7_03_v3 1030822 - 7433 -0.994 -1.486 -0.503 4.088 -3.114 3.38e-03 5.09e-02 -1.874 erythrocyte membrane protein 1, PfEMP1 VAR
185 PF3D7_0717200 Pf3D7_07_v3 745191 - 1473 -1.486 -1.798 -1.174 6.245 -3.143 3.39e-03 5.09e-02 -2.041 conserved Plasmodium protein, unknown function NA
350 PF3D7_1133000 Pf3D7_11_v3 1275574 + 90 1.218 0.798 1.639 0.916 3.117 3.36e-03 5.09e-02 -1.777 conserved Plasmodium protein, unknown function NA
471 PF3D7_1346400 Pf3D7_13_v3 1852898 + 17967 -0.515 -1.373 0.343 7.880 -3.116 3.37e-03 5.09e-02 -2.164 conserved Plasmodium protein, unknown function NA
139 PF3D7_0607000 Pf3D7_06_v3 293864 + 2934 -0.455 -0.867 -0.043 10.493 -3.110 3.42e-03 5.10e-02 -2.226 translation initiation factor IF-2, putative NA
478 PF3D7_1353300 Pf3D7_13_v3 2132068 - 6516 -0.559 -0.936 -0.182 4.337 -3.110 3.42e-03 5.10e-02 -1.917 conserved Plasmodium protein, unknown function NA
338 PF3D7_1122300 Pf3D7_11_v3 846929 + 1086 0.930 0.523 1.338 3.822 3.108 3.44e-03 5.11e-02 -1.877 conserved Plasmodium protein, unknown function NA
168 PF3D7_0707700 Pf3D7_07_v3 357700 + 2886 0.405 -0.286 1.095 7.727 3.103 3.49e-03 5.16e-02 -2.191 E3 ubiquitin-protein ligase, putative NA
313 PF3D7_1039000 Pf3D7_10_v3 1568709 + 3107 -0.863 -1.648 -0.078 8.303 -3.112 3.50e-03 5.16e-02 -2.178 serine/threonine protein kinase, FIKK family FIKK10.2
295 PF3D7_1018300 Pf3D7_10_v3 729809 - 3048 0.658 0.037 1.280 7.546 3.099 3.53e-03 5.18e-02 -2.187 conserved Plasmodium protein, unknown function NA
298 PF3D7_1019300 Pf3D7_10_v3 774929 - 5559 0.836 0.550 1.123 4.343 3.098 3.54e-03 5.18e-02 -1.925 zinc finger protein, putative NA
348 PF3D7_1131200 Pf3D7_11_v3 1199253 + 2553 -1.295 -1.897 -0.693 2.053 -3.094 3.59e-03 5.24e-02 -1.861 conserved Plasmodium protein, unknown function NA
31 PF3D7_0300200 Pf3D7_03_v3 46369 - 1211 -1.606 -2.102 -1.111 0.105 -3.084 3.67e-03 5.30e-02 -1.858 rifin RIF
490 PF3D7_1364300 Pf3D7_13_v3 2579159 - 3456 0.508 0.165 0.851 6.964 3.086 3.65e-03 5.30e-02 -2.185 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 PRP16
516 PF3D7_1414100 Pf3D7_14_v3 560093 + 2232 0.593 -0.128 1.314 6.951 3.085 3.67e-03 5.30e-02 -2.185 conserved Plasmodium protein, unknown function NA
59 PF3D7_0404300 Pf3D7_04_v3 234014 - 3000 -0.909 -1.560 -0.257 7.649 -3.089 3.73e-03 5.31e-02 -2.234 conserved Plasmodium protein, unknown function NA
94 PF3D7_0509800 Pf3D7_05_v3 410268 + 5041 -0.353 -1.775 1.070 8.261 -3.079 3.73e-03 5.31e-02 -2.275 phosphatidylinositol 4-kinase PI4K
134 PF3D7_0601600 Pf3D7_06_v3 68833 - 861 1.190 0.854 1.527 1.022 3.079 3.72e-03 5.31e-02 -1.861 tetratricopeptide repeat protein, putative NA
275 PF3D7_1002300 Pf3D7_10_v3 117242 + 1293 0.952 -0.352 2.255 1.443 3.078 3.73e-03 5.31e-02 -1.865 conserved Plasmodium protein, unknown function NA
128 PF3D7_0528800 Pf3D7_05_v3 1180425 - 1614 0.448 -0.366 1.262 6.042 3.075 3.77e-03 5.35e-02 -2.139 nucleolar preribosomal GTPase, putative NA
120 PF3D7_0524400 Pf3D7_05_v3 1013453 - 1098 0.865 0.219 1.511 6.191 3.074 3.81e-03 5.39e-02 -2.157 ribosome-interacting GTPase 1, putative RBG1
258 PF3D7_0922100 Pf3D7_09_v3 895415 + 4890 -0.473 -0.673 -0.274 10.500 -3.069 3.83e-03 5.39e-02 -2.327 ubiquitin-like protein, putative NA
10 PF3D7_0115200 Pf3D7_01_v3 591849 + 1339 -2.160 -2.833 -1.487 -0.510 -3.072 3.87e-03 5.42e-02 -1.914 rifin RIF
375 PF3D7_1210300 Pf3D7_12_v3 465115 + 630 0.735 0.280 1.189 3.502 3.066 3.86e-03 5.42e-02 -1.955 conserved Plasmodium protein, unknown function NA
257 PF3D7_0921900 Pf3D7_09_v3 888559 + 747 -0.520 -0.912 -0.129 6.911 -3.062 3.90e-03 5.44e-02 -2.242 conserved Plasmodium protein, unknown function NA
349 PF3D7_1132300 Pf3D7_11_v3 1253073 + 822 0.867 0.243 1.491 2.387 3.059 3.93e-03 5.47e-02 -1.929 nucleic acid binding protein, putative NA
325 PF3D7_1108600 Pf3D7_11_v3 369675 - 1032 -0.688 -1.013 -0.362 9.245 -3.056 4.00e-03 5.48e-02 -2.350 endoplasmic reticulum-resident calcium binding protein ERC
346 PF3D7_1127000 Pf3D7_11_v3 1056198 - 1857 -0.592 -1.048 -0.137 6.998 -3.053 3.99e-03 5.48e-02 -2.265 protein phosphatase, putative NA
464 PF3D7_1336700 Pf3D7_13_v3 1482361 - 477 0.629 0.304 0.955 7.531 3.056 3.97e-03 5.48e-02 -2.291 conserved Plasmodium protein, unknown function NA
501 PF3D7_1401600 Pf3D7_14_v3 61364 - 1625 -0.647 -1.129 -0.166 8.941 -3.054 4.01e-03 5.48e-02 -2.354 Plasmodium exported protein (PHISTb), unknown function NA
560 PF3D7_1451100 Pf3D7_14_v3 2090902 + 2499 -0.618 -1.411 0.175 12.579 -3.052 4.00e-03 5.48e-02 -2.354 elongation factor 2 eEF2
266 PF3D7_0931000 Pf3D7_09_v3 1248866 - 2736 1.104 0.394 1.813 2.571 3.048 4.05e-03 5.52e-02 -1.957 elongation factor Tu, putative NA
249 PF3D7_0913100 Pf3D7_09_v3 571031 - 2319 1.128 0.659 1.596 -0.224 3.043 4.10e-03 5.55e-02 -1.951 conserved Plasmodium protein, unknown function NA
504 PF3D7_1403900 Pf3D7_14_v3 142242 - 897 -0.742 -1.681 0.197 4.660 -3.043 4.10e-03 5.55e-02 -2.132 serine/threonine protein phosphatase CPPED1, putative CPPED1
217 PF3D7_0818000 Pf3D7_08_v3 821334 + 1119 0.720 0.222 1.219 6.278 3.041 4.12e-03 5.56e-02 -2.236 conserved protein, unknown function NA
363 PF3D7_1149200 Pf3D7_11_v3 1976407 + 3398 -1.041 -1.909 -0.173 9.787 -3.056 4.18e-03 5.63e-02 -2.356 ring-infected erythrocyte surface antigen NA
337 PF3D7_1121600 Pf3D7_11_v3 815386 - 937 -0.509 -1.042 0.024 10.612 -3.032 4.23e-03 5.67e-02 -2.420 exported protein 1 EXP1
531 PF3D7_1426200 Pf3D7_14_v3 1021652 - 1206 -0.447 -0.794 -0.101 7.961 -3.027 4.28e-03 5.72e-02 -2.389 protein arginine N-methyltransferase 1 PRMT1
392 PF3D7_1225200 Pf3D7_12_v3 1024455 - 3564 0.388 -0.237 1.013 6.864 3.023 4.33e-03 5.77e-02 -2.334 conserved Plasmodium protein, unknown function NA
373 PF3D7_1207100 Pf3D7_12_v3 324336 - 2523 -0.473 -0.846 -0.100 8.689 -3.017 4.40e-03 5.82e-02 -2.438 small subunit rRNA processing factor, putative NA
450 PF3D7_1319300 Pf3D7_13_v3 795939 - 2415 0.353 -0.504 1.210 7.942 3.017 4.40e-03 5.82e-02 -2.407 N2,N2-dimethylguanosine tRNA methyltransferase, putative NA
143 PF3D7_0612900 Pf3D7_06_v3 531126 + 2061 -0.376 -1.106 0.354 9.170 -3.014 4.44e-03 5.86e-02 -2.456 nucleolar GTP-binding protein 1, putative NA
83 PF3D7_0424900 Pf3D7_04_v3 1127779 + 1024 -0.621 -1.267 0.026 8.713 -3.004 4.56e-03 5.97e-02 -2.459 Plasmodium exported protein (PHISTa), unknown function NA
108 PF3D7_0518500 Pf3D7_05_v3 763532 - 3372 -0.459 -1.062 0.143 8.229 -3.006 4.54e-03 5.97e-02 -2.454 ATP-dependent RNA helicase DDX23, putative DDX23
300 PF3D7_1022400 Pf3D7_10_v3 939938 - 2297 -0.623 -0.877 -0.369 9.102 -3.005 4.56e-03 5.97e-02 -2.478 serine/arginine-rich splicing factor 4 SRSF4
189 PF3D7_0720200 Pf3D7_07_v3 879454 + 493 -0.541 -1.480 0.398 4.827 -3.001 4.59e-03 5.98e-02 -2.202 conserved Plasmodium protein, unknown function NA
284 PF3D7_1012000 Pf3D7_10_v3 463493 + 3514 -0.531 -0.908 -0.154 6.112 -2.998 4.63e-03 5.99e-02 -2.336 E3 ubiquitin-protein ligase, putative NA
287 PF3D7_1014700 Pf3D7_10_v3 595308 + 915 -0.767 -1.076 -0.458 3.527 -2.997 4.64e-03 5.99e-02 -2.168 prohibitin, putative NA
401 PF3D7_1232200 Pf3D7_12_v3 1333134 + 1763 -0.964 -1.289 -0.639 0.873 -2.996 4.65e-03 5.99e-02 -2.047 dihydrolipoyl dehydrogenase, mitochondrial LPD1
572 PF3D7_1460500 Pf3D7_14_v3 2466091 + 4899 0.945 -0.112 2.003 2.462 2.996 4.66e-03 5.99e-02 -2.071 conserved Plasmodium protein, unknown function NA
282 PF3D7_1009900 Pf3D7_10_v3 399207 + 2572 0.775 0.279 1.272 3.916 2.990 4.73e-03 6.07e-02 -2.156 conserved Plasmodium protein, unknown function NA
37 PF3D7_0305000 Pf3D7_03_v3 234058 - 1277 0.734 0.417 1.051 3.430 2.985 4.79e-03 6.09e-02 -2.158 elongation factor Ts EF-Ts
70 PF3D7_0415300 Pf3D7_04_v3 681810 + 4159 -0.512 -0.922 -0.103 8.667 -2.986 4.78e-03 6.09e-02 -2.513 cdc2-related protein kinase 3 CRK3
496 PF3D7_1368500 Pf3D7_13_v3 2722690 + 2493 1.037 0.748 1.325 0.223 2.985 4.79e-03 6.09e-02 -2.070 conserved Plasmodium protein, unknown function NA
376 PF3D7_1211000 Pf3D7_12_v3 484065 + 5838 -1.213 -1.654 -0.773 0.530 -2.983 4.82e-03 6.11e-02 -2.073 kinesin-7, putative NA
233 PF3D7_0830900 Pf3D7_08_v3 1317600 - 742 -0.885 -1.343 -0.426 4.631 -2.983 4.84e-03 6.11e-02 -2.271 Plasmodium exported protein, unknown function NA
263 PF3D7_0926000 Pf3D7_09_v3 1043542 + 4253 0.754 -0.393 1.900 3.345 2.981 4.85e-03 6.11e-02 -2.140 protein kinase, putative NA
312 PF3D7_1037900 Pf3D7_10_v3 1502955 - 1368 0.957 0.577 1.338 2.108 2.975 4.92e-03 6.18e-02 -2.115 conserved Plasmodium protein, unknown function NA
51 PF3D7_0321000 Pf3D7_03_v3 877735 + 1777 -0.811 -1.143 -0.479 4.629 -2.970 4.99e-03 6.23e-02 -2.252 conserved Plasmodium protein, unknown function NA
384 PF3D7_1217000 Pf3D7_12_v3 674349 - 429 0.921 0.367 1.475 1.664 2.970 4.99e-03 6.23e-02 -2.111 conserved Plasmodium protein, unknown function NA
385 PF3D7_1217300 Pf3D7_12_v3 682837 + 2886 0.667 0.061 1.273 6.184 2.965 5.05e-03 6.25e-02 -2.409 GTP-binding protein, putative NA
410 PF3D7_1243900 Pf3D7_12_v3 1834064 - 6673 -1.332 -1.711 -0.953 0.596 -2.965 5.05e-03 6.25e-02 -2.111 double C2-like domain-containing protein DOC2
434 PF3D7_1302900 Pf3D7_13_v3 154992 + 2403 0.967 0.329 1.604 3.551 2.965 5.05e-03 6.25e-02 -2.203 conserved Plasmodium protein, unknown function NA
429 PF3D7_1253100 Pf3D7_12_v3 2171342 + 1008 0.565 -0.066 1.197 6.955 2.961 5.10e-03 6.29e-02 -2.491 Plasmodium exported protein (PHISTa), unknown function NA
27 PF3D7_0220300 Pf3D7_02_v3 813827 - 828 -1.012 -1.660 -0.365 3.876 -2.961 5.14e-03 6.30e-02 -2.274 Plasmodium exported protein, unknown function NA
56 PF3D7_0400700 Pf3D7_04_v3 63104 - 1373 -2.029 -2.511 -1.546 -0.462 -2.964 5.14e-03 6.30e-02 -2.134 rifin RIF
243 PF3D7_0906000 Pf3D7_09_v3 298665 - 5515 -0.750 -3.134 1.634 3.414 -2.957 5.17e-03 6.30e-02 -2.237 exoribonuclease II RNaseII
487 PF3D7_1361200 Pf3D7_13_v3 2455261 + 6164 -0.369 -0.685 -0.052 7.951 -2.958 5.16e-03 6.30e-02 -2.561 conserved Plasmodium protein, unknown function NA
135 PF3D7_0604500 Pf3D7_06_v3 189012 + 9067 -0.561 -0.890 -0.232 11.003 -2.954 5.21e-03 6.30e-02 -2.609 conserved Plasmodium protein, unknown function NA
237 PF3D7_0833500 Pf3D7_08_v3 1435794 - 7656 -0.964 -1.526 -0.403 4.351 -2.953 5.22e-03 6.30e-02 -2.271 erythrocyte membrane protein 1, PfEMP1 VAR
465 PF3D7_1341100 Pf3D7_13_v3 1632602 - 108 -1.057 -1.456 -0.659 3.016 -2.954 5.21e-03 6.30e-02 -2.180 U6 spliceosomal RNA NA
202 PF3D7_0803100 Pf3D7_08_v3 199181 - 3738 -0.554 -1.417 0.308 8.102 -2.951 5.25e-03 6.33e-02 -2.579 U3 small nucleolar RNA-associated protein 14, putative UTP14
534 PF3D7_1429100 Pf3D7_14_v3 1142154 + 1638 -1.087 -1.692 -0.483 3.402 -2.951 5.28e-03 6.34e-02 -2.243 apicoplast ribosomal protein L15 precursor, putative NA
439 PF3D7_1306400 Pf3D7_13_v3 297178 - 1182 -0.451 -1.251 0.349 7.284 -2.944 5.34e-03 6.40e-02 -2.551 26S protease regulatory subunit 10B, putative RPT4
293 PF3D7_1016300 Pf3D7_10_v3 650898 - 2670 -0.743 -1.261 -0.225 6.278 -2.944 5.36e-03 6.41e-02 -2.469 glycophorin binding protein GBP
144 PF3D7_0613700 Pf3D7_06_v3 559349 - 2112 -0.721 -2.430 0.989 3.628 -2.938 5.44e-03 6.42e-02 -2.315 syntaxin binding protein, putative NA
206 PF3D7_0806600 Pf3D7_08_v3 349317 - 4046 0.530 0.151 0.909 5.537 2.938 5.43e-03 6.42e-02 -2.423 kinesin-like protein, putative NA
280 PF3D7_1005000 Pf3D7_10_v3 225456 - 2250 0.737 -0.212 1.687 3.581 2.941 5.39e-03 6.42e-02 -2.246 methionine–tRNA ligase, putative MRSapi
296 PF3D7_1018500 Pf3D7_10_v3 735921 - 893 -0.528 -0.865 -0.192 6.598 -2.939 5.41e-03 6.42e-02 -2.513 PHF5-like protein, putative NA
428 PF3D7_1252300 Pf3D7_12_v3 2128400 - 387 -0.756 -1.518 0.005 8.882 -2.943 5.46e-03 6.43e-02 -2.618 conserved Plasmodium protein, unknown function NA
61 PF3D7_0404800 Pf3D7_04_v3 264305 - 1866 1.425 0.637 2.212 2.020 2.938 5.48e-03 6.43e-02 -2.192 conserved Plasmodium protein, unknown function NA
244 PF3D7_0906600 Pf3D7_09_v3 320811 - 2532 0.483 -1.418 2.384 9.190 2.932 5.53e-03 6.45e-02 -2.654 zinc finger protein, putative NA
345 PF3D7_1126500 Pf3D7_11_v3 1033062 + 4107 0.573 -0.030 1.176 7.197 2.932 5.53e-03 6.45e-02 -2.581 conserved Plasmodium protein, unknown function NA
274 PF3D7_1001000 Pf3D7_10_v3 63152 + 881 -0.979 -1.809 -0.149 3.798 -2.933 5.54e-03 6.45e-02 -2.352 Plasmodium exported protein (hyp12), unknown function PfJ13
335 PF3D7_1120500 Pf3D7_11_v3 772539 + 2504 0.414 -0.202 1.031 6.939 2.929 5.56e-03 6.45e-02 -2.566 tRNA nucleotidyltransferase, putative NA
399 PF3D7_1230900 Pf3D7_12_v3 1267368 + 2814 -0.432 -1.171 0.308 9.390 -2.928 5.59e-03 6.47e-02 -2.663 serine/threonine protein kinase RIO1, putative RIO1
540 PF3D7_1436900 Pf3D7_14_v3 1500128 - 838 0.668 0.130 1.206 4.280 2.925 5.62e-03 6.49e-02 -2.341 histidine triad protein, putative NA
424 PF3D7_1250000 Pf3D7_12_v3 2044120 + 507 -0.587 -1.566 0.391 6.656 -2.924 5.64e-03 6.50e-02 -2.555 rRNA-processing protein, putative NA
239 PF3D7_0903100 Pf3D7_09_v3 130140 - 798 0.680 0.256 1.104 4.674 2.919 5.71e-03 6.55e-02 -2.385 protein RER1, putative RER1
26 PF3D7_0218800 Pf3D7_02_v3 766390 - 626 0.712 0.350 1.075 4.392 2.917 5.74e-03 6.56e-02 -2.359 ribonuclease P NA
503 PF3D7_1402900 Pf3D7_14_v3 106370 + 2865 1.270 0.847 1.693 -0.495 2.916 5.76e-03 6.56e-02 -2.222 conserved Plasmodium protein, unknown function NA
545 PF3D7_1441000 Pf3D7_14_v3 1669980 - 1671 0.659 0.347 0.971 4.042 2.916 5.76e-03 6.56e-02 -2.345 cytoplasmic tRNA 2-thiolation protein 2, putative NCS2
294 PF3D7_1018000 Pf3D7_10_v3 718454 + 1683 1.168 0.545 1.790 2.241 2.914 5.79e-03 6.57e-02 -2.248 tRNA pseudouridine synthase, putative NA
91 PF3D7_0507600 Pf3D7_05_v3 313199 + 1959 0.587 -0.307 1.481 6.557 2.912 5.83e-03 6.58e-02 -2.581 cell differentiation protein, putative CAF40
155 PF3D7_0625600 Pf3D7_06_v3 1039655 + 1896 0.874 0.463 1.284 5.591 2.914 5.85e-03 6.58e-02 -2.489 poly(A) polymerase PAP, putative NA
216 PF3D7_0817200 Pf3D7_08_v3 777257 - 2391 0.463 0.175 0.751 5.996 2.911 5.84e-03 6.58e-02 -2.529 conserved Plasmodium protein, unknown function NA
309 PF3D7_1033200 Pf3D7_10_v3 1335222 + 1068 -0.713 -0.952 -0.474 7.027 -2.911 5.86e-03 6.58e-02 -2.581 early transcribed membrane protein 10.2 ETRAMP10.2
58 PF3D7_0403700 Pf3D7_04_v3 206228 - 3167 -0.318 -0.856 0.219 8.454 -2.904 5.95e-03 6.65e-02 -2.708 pre-mRNA-splicing factor CLF1, putative CLF1
203 PF3D7_0803200 Pf3D7_08_v3 204241 - 2421 -1.030 -2.425 0.365 1.745 -2.902 5.97e-03 6.65e-02 -2.261 filament assembling protein, putative NA
514 PF3D7_1412700 Pf3D7_14_v3 512363 + 3660 -0.526 -1.135 0.083 5.946 -2.903 5.96e-03 6.65e-02 -2.550 AAA family ATPase, putative NA
148 PF3D7_0618200 Pf3D7_06_v3 764667 - 826 -0.492 -0.787 -0.197 7.053 -2.898 6.04e-03 6.65e-02 -2.656 conserved Plasmodium protein, unknown function NA
193 PF3D7_0723400 Pf3D7_07_v3 978920 - 4269 -0.411 -1.124 0.303 9.715 -2.898 6.03e-03 6.65e-02 -2.742 conserved Plasmodium protein, unknown function NA
288 PF3D7_1015500 Pf3D7_10_v3 624048 - 1848 0.912 0.030 1.794 0.006 2.899 6.03e-03 6.65e-02 -2.255 conserved Plasmodium protein, unknown function NA
497 PF3D7_1368600 Pf3D7_13_v3 2725669 - 279 -0.901 -1.216 -0.586 2.009 -2.896 6.07e-03 6.65e-02 -2.284 mitochondrial import inner membrane translocase subunit TIM9, putative TIM9
522 PF3D7_1417600 Pf3D7_14_v3 730694 - 13989 -0.453 -1.308 0.401 8.923 -2.897 6.05e-03 6.65e-02 -2.734 conserved Plasmodium protein, unknown function NA
535 PF3D7_1432900 Pf3D7_14_v3 1296173 - 1039 0.681 0.409 0.953 3.904 2.895 6.08e-03 6.65e-02 -2.374 SF-assemblin, putative NA
571 PF3D7_1460200 Pf3D7_14_v3 2456879 - 924 1.252 0.379 2.125 1.138 2.895 6.08e-03 6.65e-02 -2.266 conserved Plasmodium protein, unknown function NA
69 PF3D7_0412900 Pf3D7_04_v3 576810 - 7859 -1.033 -1.344 -0.722 2.642 -2.894 6.10e-03 6.65e-02 -2.305 erythrocyte membrane protein 1, PfEMP1 VAR
49 PF3D7_0319600 Pf3D7_03_v3 817913 + 783 -0.419 -0.965 0.128 8.342 -2.891 6.15e-03 6.67e-02 -2.737 elongation factor 1 (EF-1), putative NA
444 PF3D7_1309400 Pf3D7_13_v3 431892 + 3984 -0.653 -1.269 -0.037 5.709 -2.891 6.14e-03 6.67e-02 -2.550 HORMA domain protein, putative NA
395 PF3D7_1227800 Pf3D7_12_v3 1134370 - 3279 -0.355 -0.694 -0.017 9.186 -2.890 6.17e-03 6.67e-02 -2.755 histone S-adenosyl methyltransferase, putative NA
538 PF3D7_1436000 Pf3D7_14_v3 1458131 + 1740 -0.526 -1.586 0.533 8.085 -2.885 6.25e-03 6.74e-02 -2.702 glucose-6-phosphate isomerase GPI
520 PF3D7_1416300 Pf3D7_14_v3 659539 + 1365 0.945 0.145 1.745 1.326 2.884 6.27e-03 6.75e-02 -2.294 conserved protein, unknown function NA
71 PF3D7_0416000 Pf3D7_04_v3 701526 - 2637 -0.645 -1.233 -0.058 6.301 -2.883 6.29e-03 6.75e-02 -2.630 RNA-binding protein, putative NA
75 PF3D7_0417800 Pf3D7_04_v3 787243 - 2100 -0.976 -1.845 -0.107 3.420 -2.879 6.36e-03 6.81e-02 -2.434 cdc2-related protein kinase 1 CRK1
117 PF3D7_0523300 Pf3D7_05_v3 970266 - 697 0.927 0.217 1.636 0.675 2.877 6.38e-03 6.81e-02 -2.301 conserved Plasmodium protein, unknown function NA
250 PF3D7_0913200 Pf3D7_09_v3 575679 + 831 -0.479 -1.061 0.103 8.889 -2.869 6.51e-03 6.92e-02 -2.802 elongation factor 1-beta EF-1beta
407 PF3D7_1240600 Pf3D7_12_v3 1719574 + 7883 -1.239 -1.568 -0.911 3.783 -2.876 6.51e-03 6.92e-02 -2.421 erythrocyte membrane protein 1, PfEMP1 VAR
113 PF3D7_0521800 Pf3D7_05_v3 885714 + 2519 0.974 0.248 1.700 1.517 2.865 6.58e-03 6.95e-02 -2.337 nucleotide binding protein, putative NA
573 PF3D7_1461600 Pf3D7_14_v3 2498047 - 2338 -0.535 -2.218 1.149 8.956 -2.866 6.57e-03 6.95e-02 -2.809 splicing factor 3B subunit 2, putative SF3B2
87 PF3D7_0502400 Pf3D7_05_v3 109898 - 1794 0.704 0.466 0.942 7.883 2.865 6.65e-03 6.99e-02 -2.776 merozoite surface protein 8 MSP8
354 PF3D7_1137100 Pf3D7_11_v3 1462168 + 903 0.544 -0.168 1.256 5.368 2.861 6.65e-03 6.99e-02 -2.586 mitochondrial ribosomal protein S9 precursor, putative NA
371 PF3D7_1206200 Pf3D7_12_v3 275744 - 3593 -0.499 -0.804 -0.193 10.135 -2.859 6.70e-03 7.02e-02 -2.840 eukaryotic translation initiation factor 3 subunit C, putative EIF3C
34 PF3D7_0303400 Pf3D7_03_v3 178420 + 2708 0.968 0.445 1.490 1.373 2.854 6.77e-03 7.03e-02 -2.358 palmitoyltransferase DHHC1 DHHC1
109 PF3D7_0519400 Pf3D7_05_v3 798036 - 740 -0.466 -0.773 -0.159 9.741 -2.857 6.72e-03 7.03e-02 -2.841 40S ribosomal protein S24 RPS24
360 PF3D7_1143800 Pf3D7_11_v3 1748439 + 2700 0.520 0.161 0.880 6.960 2.853 6.80e-03 7.03e-02 -2.750 conserved Plasmodium protein, unknown function NA
367 PF3D7_1202900 Pf3D7_12_v3 162429 - 294 -0.574 -0.891 -0.258 9.229 -2.853 6.80e-03 7.03e-02 -2.846 high mobility group protein B1 HMGB1
468 PF3D7_1344900 Pf3D7_13_v3 1801271 + 4467 0.419 0.090 0.749 8.107 2.855 6.76e-03 7.03e-02 -2.808 conserved Plasmodium protein, unknown function NA
570 PF3D7_1459300 Pf3D7_14_v3 2432177 + 570 0.745 0.128 1.362 1.769 2.856 6.75e-03 7.03e-02 -2.369 OPA3-like protein, putative NA
124 PF3D7_0527500 Pf3D7_05_v3 1143618 + 1742 -0.358 -0.736 0.019 9.602 -2.850 6.84e-03 7.05e-02 -2.855 Hsc70-interacting protein HIP
483 PF3D7_1358700 Pf3D7_13_v3 2326394 - 462 0.759 0.391 1.127 5.919 2.851 6.85e-03 7.05e-02 -2.671 YOP1-like protein, putative YOP1L
116 PF3D7_0523200 Pf3D7_05_v3 966123 + 3615 0.968 0.440 1.495 1.317 2.846 6.91e-03 7.06e-02 -2.376 conserved Plasmodium protein, unknown function NA
270 PF3D7_0935600 Pf3D7_09_v3 1405192 + 1831 -1.141 -1.561 -0.720 9.813 -2.868 6.92e-03 7.06e-02 -2.811 gametocytogenesis-implicated protein GIG
397 PF3D7_1229600 Pf3D7_12_v3 1214043 - 3673 -0.941 -1.789 -0.094 1.439 -2.844 6.95e-03 7.06e-02 -2.381 conserved Plasmodium protein, unknown function NA
486 PF3D7_1361000 Pf3D7_13_v3 2445090 - 2175 0.820 -0.143 1.783 4.682 2.843 6.97e-03 7.06e-02 -2.561 protein arginine N-methyltransferase 5, putative PRMT5
491 PF3D7_1365000 Pf3D7_13_v3 2608698 + 1047 -0.778 -1.316 -0.241 3.911 -2.844 6.95e-03 7.06e-02 -2.483 conserved Plasmodium protein, unknown function NA
576 PF3D7_1467300 Pf3D7_14_v3 2750958 + 1467 0.888 0.495 1.281 2.920 2.843 6.97e-03 7.06e-02 -2.431 1-deoxy-D-xylulose 5-phosphate reductoisomerase DXR
33 PF3D7_0303200 Pf3D7_03_v3 169571 + 4730 -0.698 -1.308 -0.088 3.533 -2.836 7.10e-03 7.07e-02 -2.512 HAD superfamily protein, putative NA
104 PF3D7_0517200 Pf3D7_05_v3 720743 - 1899 0.627 0.255 1.000 7.316 2.838 7.07e-03 7.07e-02 -2.802 conserved Plasmodium protein, unknown function NA
228 PF3D7_0826900 Pf3D7_08_v3 1164655 + 2551 0.978 -0.074 2.030 3.039 2.838 7.07e-03 7.07e-02 -2.447 conserved Plasmodium protein, unknown function NA
386 PF3D7_1217400 Pf3D7_12_v3 686307 - 2565 0.869 0.526 1.211 5.197 2.838 7.10e-03 7.07e-02 -2.622 conserved Plasmodium protein, unknown function NA
519 PF3D7_1415600 Pf3D7_14_v3 629419 - 3477 -0.575 -0.904 -0.246 4.156 -2.838 7.06e-03 7.07e-02 -2.565 conserved Plasmodium protein, unknown function NA
546 PF3D7_1443300 Pf3D7_14_v3 1776010 + 653 -0.453 -0.885 -0.022 6.719 -2.838 7.06e-03 7.07e-02 -2.770 U6 snRNA-associated Sm-like protein LSm5, putative LSM5
562 PF3D7_1452100 Pf3D7_14_v3 2141662 + 1017 0.904 0.547 1.261 2.378 2.839 7.05e-03 7.07e-02 -2.423 leucine-rich repeat protein LRR3
515 PF3D7_1413800 Pf3D7_14_v3 547954 + 1464 0.339 -0.386 1.064 6.476 2.828 7.26e-03 7.21e-02 -2.774 diphthamide biosynthesis protein 1, putative DPH1
57 PF3D7_0403600 Pf3D7_04_v3 197846 - 3363 -1.163 -1.574 -0.753 2.273 -2.828 7.28e-03 7.21e-02 -2.467 conserved Plasmodium protein, unknown function NA
23 PF3D7_0211800 Pf3D7_02_v3 475242 + 1833 -0.587 -1.433 0.260 9.276 -2.823 7.37e-03 7.28e-02 -2.916 asparagine–tRNA ligase AsnRS
121 PF3D7_0524500 Pf3D7_05_v3 1016198 + 372 1.006 0.247 1.764 2.180 2.819 7.43e-03 7.28e-02 -2.457 conserved Plasmodium protein, unknown function NA
123 PF3D7_0527300 Pf3D7_05_v3 1135976 - 1895 0.530 0.138 0.922 6.450 2.815 7.51e-03 7.28e-02 -2.797 methionine aminopeptidase 1a, putative METAP1a
157 PF3D7_0626800 Pf3D7_06_v3 1078995 + 2326 -0.591 -1.198 0.017 11.922 -2.818 7.48e-03 7.28e-02 -2.932 pyruvate kinase PyrK
218 PF3D7_0819100 Pf3D7_08_v3 869562 + 1013 0.442 -0.140 1.024 5.546 2.820 7.41e-03 7.28e-02 -2.702 BRIX domain, putative NA
241 PF3D7_0905200 Pf3D7_09_v3 245261 - 3600 0.460 -0.410 1.331 6.224 2.815 7.50e-03 7.28e-02 -2.779 mitochondrial carrier protein, putative NA
524 PF3D7_1419000 Pf3D7_14_v3 786958 - 3501 0.773 -0.008 1.555 3.397 2.819 7.43e-03 7.28e-02 -2.510 conserved Plasmodium protein, unknown function NA
579 PF3D7_1469900 Pf3D7_14_v3 2866358 + 1826 -1.223 -1.484 -0.963 0.011 -2.816 7.49e-03 7.28e-02 -2.427 conserved Plasmodium protein, unknown function NA
581 PF3D7_1472000 Pf3D7_14_v3 2940478 + 1126 -0.532 -1.067 0.002 5.896 -2.816 7.48e-03 7.28e-02 -2.737 pre-mRNA-splicing factor ISY1, putative ISY1
17 PF3D7_0202500 Pf3D7_02_v3 127994 + 321 -0.625 -1.245 -0.005 12.135 -2.813 7.60e-03 7.33e-02 -2.942 early transcribed membrane protein 2 ETRAMP2
473 PF3D7_1347500 Pf3D7_13_v3 1897983 - 1380 -0.435 -1.098 0.228 12.066 -2.811 7.59e-03 7.33e-02 -2.945 DNA/RNA-binding protein Alba 4 ALBA4
569 PF3D7_1459100 Pf3D7_14_v3 2423907 + 2394 1.078 0.676 1.480 1.903 2.810 7.60e-03 7.33e-02 -2.466 GTP-binding protein, putative NA
409 PF3D7_1242900 Pf3D7_12_v3 1808878 - 745 0.885 0.532 1.238 0.857 2.809 7.62e-03 7.33e-02 -2.450 mitochondrial import inner membrane translocase subunit TIM13, putative TIM13
278 PF3D7_1004100 Pf3D7_10_v3 182244 + 4857 1.182 0.860 1.504 3.140 2.806 7.73e-03 7.41e-02 -2.534 hypothetical protein NA
548 PF3D7_1445300 Pf3D7_14_v3 1860148 + 1948 0.760 0.075 1.446 3.421 2.802 7.75e-03 7.42e-02 -2.546 mitochondrial ribosomal protein S29 precursor, putative NA
138 PF3D7_0606900 Pf3D7_06_v3 290426 - 660 0.980 -0.161 2.121 3.885 2.802 7.78e-03 7.43e-02 -2.596 glutaredoxin-like protein GLP2
142 PF3D7_0612800 Pf3D7_06_v3 528060 - 1116 0.778 -0.966 2.523 3.897 2.798 7.84e-03 7.47e-02 -2.595 6-cysteine protein P12p
406 PF3D7_1240400 Pf3D7_12_v3 1704512 + 7979 -0.896 -1.428 -0.364 4.878 -2.798 7.88e-03 7.49e-02 -2.682 erythrocyte membrane protein 1, PfEMP1 VAR
80 PF3D7_0421300 Pf3D7_04_v3 969031 - 7561 -1.049 -1.816 -0.283 4.771 -2.800 7.92e-03 7.51e-02 -2.673 erythrocyte membrane protein 1, PfEMP1 VAR
24 PF3D7_0216400 Pf3D7_02_v3 675431 + 2169 0.686 0.320 1.052 0.562 2.787 8.05e-03 7.61e-02 -2.488 vacuolar protein sorting-associated protein 45, putative VPS45
377 PF3D7_1211200 Pf3D7_12_v3 491893 - 5496 -0.455 -0.978 0.069 7.015 -2.787 8.07e-03 7.61e-02 -2.905 conserved Plasmodium protein, unknown function NA
498 PF3D7_1370300 Pf3D7_13_v3 2787972 + 942 -0.743 -1.526 0.041 11.370 -2.794 8.09e-03 7.62e-02 -3.001 membrane associated histidine-rich protein MAHRP1
245 PF3D7_0907400 Pf3D7_09_v3 351955 - 2769 -0.479 -1.407 0.449 8.348 -2.784 8.13e-03 7.64e-02 -2.973 ATP-dependent protease ATPase subunit ClpY ClpY
530 PF3D7_1426100 Pf3D7_14_v3 1018745 - 516 0.385 -0.100 0.869 7.977 2.783 8.15e-03 7.64e-02 -2.974 basic transcription factor 3b, putative NA
223 PF3D7_0822300 Pf3D7_08_v3 988281 - 483 0.532 0.128 0.937 4.939 2.781 8.18e-03 7.65e-02 -2.726 small nuclear ribonucleoprotein G, putative SNRPG
195 PF3D7_0724000 Pf3D7_07_v3 1006335 + 5811 0.840 0.470 1.211 2.272 2.779 8.22e-03 7.67e-02 -2.545 Rab GTPase activator and protein kinase, putative NA
261 PF3D7_0924600 Pf3D7_09_v3 999463 + 6383 -1.220 -1.505 -0.935 0.790 -2.777 8.26e-03 7.70e-02 -2.515 conserved Plasmodium protein, unknown function NA
149 PF3D7_0621300 Pf3D7_06_v3 873809 + 2382 0.383 -0.299 1.064 7.567 2.776 8.31e-03 7.70e-02 -2.972 mRNA binding Pumilio-homology domain protein, putative NA
508 PF3D7_1406200 Pf3D7_14_v3 217845 + 8463 -0.453 -1.583 0.677 9.513 -2.775 8.31e-03 7.70e-02 -3.031 conserved Plasmodium protein, unknown function NA
574 PF3D7_1462800 Pf3D7_14_v3 2559098 + 1250 -0.626 -1.385 0.132 13.115 -2.776 8.34e-03 7.72e-02 -3.015 glyceraldehyde-3-phosphate dehydrogenase GAPDH
306 PF3D7_1027500 Pf3D7_10_v3 1147866 + 348 0.923 0.672 1.174 0.639 2.771 8.40e-03 7.75e-02 -2.524 conserved Plasmodium protein, unknown function NA
35 PF3D7_0304300 Pf3D7_03_v3 212283 + 4290 1.106 0.823 1.389 1.180 2.768 8.46e-03 7.76e-02 -2.537 conserved Plasmodium protein, unknown function NA
73 PF3D7_0416200 Pf3D7_04_v3 709460 - 624 -1.454 -1.984 -0.924 2.998 -2.777 8.43e-03 7.76e-02 -2.582 conserved protein, unknown function NA
174 PF3D7_0708900 Pf3D7_07_v3 399290 - 954 0.770 0.472 1.068 4.297 2.767 8.48e-03 7.76e-02 -2.704 Cg3 protein NA
502 PF3D7_1402300 Pf3D7_14_v3 85883 - 2001 0.445 0.077 0.813 6.935 2.768 8.48e-03 7.76e-02 -2.955 26S proteasome regulatory subunit RPN6 RPN6
324 PF3D7_1107800 Pf3D7_11_v3 329867 - 5735 -0.728 -1.456 0.000 8.457 -2.765 8.65e-03 7.89e-02 -3.001 transcription factor with AP2 domain(s) ApiAP2
191 PF3D7_0721700 Pf3D7_07_v3 935497 + 1404 0.843 0.100 1.585 2.869 2.756 8.72e-03 7.95e-02 -2.621 secreted ookinete protein, putative PSOP1
236 PF3D7_0831750 Pf3D7_08_v3 1371847 + 874 1.027 0.335 1.718 2.561 2.753 8.81e-03 7.95e-02 -2.614 Plasmodium exported protein (PHISTa), unknown function, pseudogene NA
315 PF3D7_1102600 Pf3D7_11_v3 123818 - 919 1.279 0.897 1.661 2.320 2.755 8.81e-03 7.95e-02 -2.609 Plasmodium exported protein, unknown function GEXP14
459 PF3D7_1332000 Pf3D7_13_v3 1325913 - 1620 0.574 0.239 0.910 4.779 2.755 8.75e-03 7.95e-02 -2.778 syntaxin, Qa-SNARE family SYN5
537 PF3D7_1435400 Pf3D7_14_v3 1433738 - 573 0.388 -0.187 0.963 6.059 2.754 8.79e-03 7.95e-02 -2.908 ER membrane protein complex subunit 4, putative EMC4
192 PF3D7_0722300 Pf3D7_07_v3 949449 - 3666 0.483 0.218 0.749 6.531 2.749 8.89e-03 8.01e-02 -2.961 ubiquitin carboxyl-terminal hydrolase, putative NA
40 PF3D7_0311600 Pf3D7_03_v3 499602 + 2752 1.038 0.746 1.331 2.539 2.744 9.00e-03 8.09e-02 -2.635 dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1, putative NA
101 PF3D7_0516100 Pf3D7_05_v3 667486 + 7376 0.809 -0.170 1.787 3.482 2.740 9.09e-03 8.09e-02 -2.688 cation-transporting ATPase 1 ATPase1
178 PF3D7_0711700 Pf3D7_07_v3 511950 - 7476 -0.789 -1.093 -0.485 4.598 -2.741 9.08e-03 8.09e-02 -2.793 erythrocyte membrane protein 1, PfEMP1 VAR
200 PF3D7_0800900 Pf3D7_08_v3 83128 + 777 -1.118 -1.653 -0.582 3.284 -2.743 9.15e-03 8.09e-02 -2.745 Plasmodium exported protein (hyp7), unknown function, pseudogene NA
211 PF3D7_0812700 Pf3D7_08_v3 633990 + 708 0.535 -0.065 1.135 5.781 2.738 9.15e-03 8.09e-02 -2.915 RNA-binding protein (U1 snRNP-like), putative NA
227 PF3D7_0826100 Pf3D7_08_v3 1113369 - 25776 -0.478 -0.970 0.014 10.241 -2.741 9.08e-03 8.09e-02 -3.117 E3 ubiquitin-protein ligase, putative NA
265 PF3D7_0929200 Pf3D7_09_v3 1167842 + 1736 0.364 -0.669 1.398 8.361 2.740 9.10e-03 8.09e-02 -3.087 RNA-binding protein, putative NA
304 PF3D7_1027100 Pf3D7_10_v3 1133838 - 2319 -0.441 -1.158 0.276 8.266 -2.736 9.18e-03 8.09e-02 -3.094 U3 small nucleolar ribonucleoprotein protein MPP10, putative MPP10
327 PF3D7_1109900 Pf3D7_11_v3 397124 + 652 -0.659 -0.936 -0.382 7.738 -2.738 9.21e-03 8.09e-02 -3.073 60S ribosomal protein L36 RPL36
415 PF3D7_1244900 Pf3D7_12_v3 1877039 + 3003 0.762 0.196 1.328 0.883 2.738 9.15e-03 8.09e-02 -2.595 conserved Plasmodium protein, unknown function NA
457 PF3D7_1330200 Pf3D7_13_v3 1275104 + 796 0.723 -0.257 1.704 2.434 2.743 9.03e-03 8.09e-02 -2.627 conserved Plasmodium protein, unknown function NA
558 PF3D7_1450600 Pf3D7_14_v3 2075586 - 1764 0.338 -0.567 1.242 6.523 2.735 9.21e-03 8.09e-02 -2.996 S-adenosylmethionine-dependent methyltransferase, putative NA
422 PF3D7_1248600 Pf3D7_12_v3 1988237 + 2509 1.120 0.763 1.478 5.174 2.743 9.26e-03 8.12e-02 -2.851 conserved Plasmodium protein, unknown function NA
5 PF3D7_0104200 Pf3D7_01_v3 182822 - 1401 1.145 -0.211 2.501 4.099 2.737 9.29e-03 8.13e-02 -2.756 StAR-related lipid transfer protein NA
229 PF3D7_0827000 Pf3D7_08_v3 1167579 - 3870 -0.328 -1.125 0.469 8.724 -2.730 9.34e-03 8.13e-02 -3.125 ATP-dependent RNA helicase DBP10, putative DBP10
414 PF3D7_1244800 Pf3D7_12_v3 1873194 - 2094 -0.383 -0.636 -0.129 7.604 -2.730 9.33e-03 8.13e-02 -3.081 cytoplasmic translation machinery associated protein, putative NA
105 PF3D7_0517600 Pf3D7_05_v3 740156 - 879 1.044 0.709 1.379 1.434 2.726 9.42e-03 8.18e-02 -2.630 F-actin-capping protein subunit beta, putative CPbeta
3 PF3D7_0100100 Pf3D7_01_v3 29510 + 7617 -0.834 -1.453 -0.215 4.119 -2.721 9.56e-03 8.20e-02 -2.780 erythrocyte membrane protein 1, PfEMP1 VAR
127 PF3D7_0528600 Pf3D7_05_v3 1176969 - 318 -0.560 -0.933 -0.186 4.198 -2.722 9.52e-03 8.20e-02 -2.786 conserved Plasmodium protein, unknown function NA
276 PF3D7_1003700 Pf3D7_10_v3 166743 - 3927 0.730 0.439 1.021 4.247 2.721 9.54e-03 8.20e-02 -2.796 conserved Plasmodium protein, unknown function NA
381 PF3D7_1214600 Pf3D7_12_v3 613561 - 1014 -0.499 -1.155 0.158 4.795 -2.724 9.48e-03 8.20e-02 -2.843 adrenodoxin-type ferredoxin, putative NA
475 PF3D7_1350100 Pf3D7_13_v3 2005962 - 1989 -0.397 -0.739 -0.055 9.200 -2.721 9.56e-03 8.20e-02 -3.156 lysine–tRNA ligase KRS1
510 PF3D7_1409600 Pf3D7_14_v3 374800 + 2307 0.745 0.012 1.478 5.160 2.723 9.51e-03 8.20e-02 -2.879 conserved Plasmodium protein, unknown function NA
65 PF3D7_0406500 Pf3D7_04_v3 334282 - 9773 -1.156 -1.624 -0.688 10.276 -2.734 9.76e-03 8.27e-02 -3.156 NYN domain-containing protein, putative NA
171 PF3D7_0708000 Pf3D7_07_v3 368707 + 2966 0.740 0.474 1.006 3.189 2.712 9.78e-03 8.27e-02 -2.740 cytoskeleton associated protein, putative NA
368 PF3D7_1203700 Pf3D7_12_v3 187146 - 1697 -0.453 -0.775 -0.130 10.884 -2.715 9.70e-03 8.27e-02 -3.173 nucleosome assembly protein NAPL
405 PF3D7_1239800 Pf3D7_12_v3 1660451 + 17304 -0.912 -1.490 -0.334 3.750 -2.715 9.71e-03 8.27e-02 -2.792 conserved Plasmodium protein, unknown function NA
426 PF3D7_1251000 Pf3D7_12_v3 2085370 - 1590 0.916 0.271 1.561 2.530 2.713 9.75e-03 8.27e-02 -2.702 conserved Plasmodium protein, unknown function NA
495 PF3D7_1366700 Pf3D7_13_v3 2666666 + 1116 1.060 0.474 1.645 1.359 2.714 9.72e-03 8.27e-02 -2.655 conserved Plasmodium protein, unknown function NA
583 PF3D7_1473900 Pf3D7_14_v3 3007601 + 2559 0.526 -0.375 1.427 7.093 2.712 9.77e-03 8.27e-02 -3.084 conserved Plasmodium protein, unknown function NA
553 PF3D7_1447100 Pf3D7_14_v3 1932421 - 780 -0.575 -0.955 -0.194 6.513 -2.708 9.86e-03 8.32e-02 -3.045 conserved Plasmodium protein, unknown function NA
99 PF3D7_0512800 Pf3D7_05_v3 548406 - 4935 -0.765 -2.202 0.672 3.153 -2.706 9.92e-03 8.35e-02 -2.779 conserved Plasmodium protein, unknown function NA
209 PF3D7_0810800 Pf3D7_08_v3 548200 + 2417 -1.010 -1.276 -0.743 7.259 -2.717 1.00e-02 8.35e-02 -3.071 hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase PPPK-DHPS
215 PF3D7_0816600 Pf3D7_08_v3 762118 - 3213 -0.947 -1.320 -0.573 5.051 -2.706 1.01e-02 8.35e-02 -2.942 chaperone protein ClpB1 ClpB1
318 PF3D7_1103000 Pf3D7_11_v3 138646 + 389 0.964 0.556 1.372 1.515 2.702 1.00e-02 8.35e-02 -2.683 conserved Plasmodium protein, unknown function NA
334 PF3D7_1120000 Pf3D7_11_v3 756192 + 4244 -0.613 -1.493 0.268 7.431 -2.706 9.97e-03 8.35e-02 -3.128 conserved Plasmodium protein, unknown function NA
344 PF3D7_1126400 Pf3D7_11_v3 1030679 + 803 -0.398 -1.015 0.219 5.816 -2.704 9.98e-03 8.35e-02 -2.994 large ribosomal subunit processing factor, putative NA
416 PF3D7_1246000 Pf3D7_12_v3 1912457 + 2139 0.861 0.471 1.251 1.962 2.702 1.00e-02 8.35e-02 -2.696 conserved Plasmodium protein, unknown function NA
418 PF3D7_1246700 Pf3D7_12_v3 1938643 + 1323 0.928 0.133 1.724 1.236 2.700 1.01e-02 8.35e-02 -2.682 conserved Plasmodium protein, unknown function NA
460 PF3D7_1332100 Pf3D7_13_v3 1329491 + 1569 1.285 0.992 1.578 -0.358 2.701 1.01e-02 8.35e-02 -2.659 conserved Plasmodium membrane protein, unknown function NA
152 PF3D7_0623300 Pf3D7_06_v3 947493 - 1152 1.080 0.385 1.776 1.961 2.698 1.01e-02 8.37e-02 -2.707 EGF-like membrane protein, putative NA
383 PF3D7_1216400 Pf3D7_12_v3 653670 + 2766 0.842 0.557 1.128 5.754 2.702 1.01e-02 8.37e-02 -2.994 conserved Plasmodium membrane protein, unknown function NA
186 PF3D7_0717400 Pf3D7_07_v3 751877 + 2256 -0.371 -0.623 -0.118 7.670 -2.695 1.02e-02 8.40e-02 -3.161 queuine tRNA-ribosyltransferase, putative NA
119 PF3D7_0523900 Pf3D7_05_v3 993433 - 1175 0.823 -0.342 1.987 4.138 2.694 1.02e-02 8.41e-02 -2.856 conserved Plasmodium membrane protein, unknown function NA
474 PF3D7_1349300 Pf3D7_13_v3 1977269 + 5424 0.542 -0.045 1.129 5.329 2.692 1.03e-02 8.42e-02 -2.970 tyrosine kinase-like protein TKL3
563 PF3D7_1452200 Pf3D7_14_v3 2143302 + 1575 0.927 0.327 1.527 0.039 2.692 1.03e-02 8.42e-02 -2.678 aminomethyltransferase, putative NA
362 PF3D7_1148600 Pf3D7_11_v3 1925942 + 7209 -3.035 -3.785 -2.285 4.294 -2.718 1.03e-02 8.42e-02 -2.821 18S ribosomal RNA NA
342 PF3D7_1126100 Pf3D7_11_v3 1018366 - 4130 0.859 0.471 1.246 1.624 2.688 1.04e-02 8.48e-02 -2.719 autophagy-related protein 7, putative ATG7
67 PF3D7_0412400 Pf3D7_04_v3 545987 - 7824 -0.809 -0.997 -0.621 3.478 -2.685 1.05e-02 8.53e-02 -2.805 erythrocyte membrane protein 1, PfEMP1 VAR
82 PF3D7_0424700 Pf3D7_04_v3 1118430 + 3985 -0.650 -1.866 0.567 9.257 -2.687 1.05e-02 8.55e-02 -3.229 serine/threonine protein kinase, FIKK family FIKK4.2
509 PF3D7_1408400 Pf3D7_14_v3 313975 - 3483 0.583 -0.068 1.235 4.984 2.681 1.06e-02 8.57e-02 -2.967 DNA repair helicase, putative NA
154 PF3D7_0625400 Pf3D7_06_v3 1032536 - 1239 0.471 0.212 0.729 7.757 2.679 1.06e-02 8.59e-02 -3.200 conserved Plasmodium protein, unknown function NA
286 PF3D7_1013500 Pf3D7_10_v3 526840 + 4609 0.790 0.184 1.396 5.066 2.679 1.06e-02 8.59e-02 -2.975 phosphoinositide-specific phospholipase C PI-PLC
421 PF3D7_1248300 Pf3D7_12_v3 1979786 - 414 1.076 0.633 1.518 1.684 2.678 1.06e-02 8.59e-02 -2.739 conserved Plasmodium membrane protein, unknown function NA
107 PF3D7_0518400 Pf3D7_05_v3 762103 - 690 1.074 0.336 1.813 -0.117 2.674 1.08e-02 8.62e-02 -2.712 cyclin, putative CYC3
214 PF3D7_0815900 Pf3D7_08_v3 743505 + 2001 0.951 0.490 1.411 0.836 2.675 1.07e-02 8.62e-02 -2.722 dihydrolipoyl dehydrogenase, apicoplast aLipDH
477 PF3D7_1352500 Pf3D7_13_v3 2093365 - 973 -0.474 -0.773 -0.175 6.587 -2.674 1.08e-02 8.62e-02 -3.142 thioredoxin-related protein, putative NA
212 PF3D7_0812800 Pf3D7_08_v3 635537 - 219 0.753 0.380 1.127 0.380 2.671 1.08e-02 8.65e-02 -2.724 conserved Plasmodium protein, unknown function NA
472 PF3D7_1347300 Pf3D7_13_v3 1893613 - 1411 0.784 -0.066 1.634 1.989 2.672 1.08e-02 8.65e-02 -2.762 conserved Plasmodium membrane protein, unknown function NA
559 PF3D7_1450700 Pf3D7_14_v3 2078488 + 1863 -0.496 -0.943 -0.049 7.376 -2.669 1.09e-02 8.68e-02 -3.202 conserved Plasmodium protein, unknown function NA
64 PF3D7_0405700 Pf3D7_04_v3 305746 - 7248 -0.675 -1.452 0.101 3.443 -2.667 1.10e-02 8.69e-02 -2.913 lysine decarboxylase, putative NA
253 PF3D7_0915300 Pf3D7_09_v3 646951 - 2166 0.725 -0.216 1.666 3.428 2.668 1.09e-02 8.69e-02 -2.845 conserved Plasmodium protein, unknown function NA
330 PF3D7_1111700 Pf3D7_11_v3 452459 - 2403 0.581 0.082 1.080 3.957 2.663 1.11e-02 8.77e-02 -2.901 conserved Plasmodium protein, unknown function NA
575 PF3D7_1466400 Pf3D7_14_v3 2714844 - 2442 0.497 -0.565 1.560 8.609 2.656 1.12e-02 8.89e-02 -3.285 transcription factor with AP2 domain(s) ApiAP2
585 PF3D7_1474700 Pf3D7_14_v3 3063191 - 2573 0.855 0.507 1.203 2.302 2.656 1.13e-02 8.89e-02 -2.817 protein kinase, putative NA
419 PF3D7_1247400 Pf3D7_12_v3 1955124 - 915 -0.542 -0.882 -0.202 6.290 -2.654 1.13e-02 8.91e-02 -3.159 peptidyl-prolyl cis-trans isomerase FKBP35 FKBP35
430 PF3D7_1253200 Pf3D7_12_v3 2173799 - 524 -1.162 -2.604 0.279 -0.284 -2.654 1.13e-02 8.91e-02 -2.752 hypothetical protein NA
301 PF3D7_1023000 Pf3D7_10_v3 961066 - 1242 0.753 -0.184 1.690 1.353 2.652 1.14e-02 8.92e-02 -2.784 conserved Plasmodium membrane protein, unknown function NA
461 PF3D7_1333400 Pf3D7_13_v3 1370083 + 717 0.555 0.015 1.095 6.775 2.652 1.14e-02 8.92e-02 -3.198 conserved protein, unknown function NA
95 PF3D7_0510500 Pf3D7_05_v3 445983 - 2520 -0.558 -1.644 0.528 5.623 -2.647 1.15e-02 9.00e-02 -3.114 topoisomerase I TopoI
230 PF3D7_0827800 Pf3D7_08_v3 1198858 + 7200 -0.449 -1.217 0.320 7.831 -2.646 1.15e-02 9.01e-02 -3.284 SET domain protein, putative SET3
256 PF3D7_0918900 Pf3D7_09_v3 777558 + 3192 0.467 -0.229 1.163 7.837 2.645 1.16e-02 9.01e-02 -3.282 gamma-glutamylcysteine synthetase gammaGCS
146 PF3D7_0615000 Pf3D7_06_v3 622272 + 441 -0.676 -0.916 -0.437 3.668 -2.641 1.17e-02 9.03e-02 -2.911 conserved Plasmodium protein, unknown function NA
175 PF3D7_0709200 Pf3D7_07_v3 412343 - 819 0.795 0.496 1.095 1.276 2.641 1.17e-02 9.03e-02 -2.805 glutaredoxin-like protein GLP3
527 PF3D7_1423200 Pf3D7_14_v3 933059 + 2299 -0.492 -1.236 0.253 5.923 -2.641 1.17e-02 9.03e-02 -3.154 peptidyl-prolyl cis-trans isomerase CYP52
543 PF3D7_1439700 Pf3D7_14_v3 1613853 - 1690 0.905 0.618 1.192 0.191 2.641 1.17e-02 9.03e-02 -2.784 leucine carboxyl methyltransferase, putative NA
556 PF3D7_1450100 Pf3D7_14_v3 2051621 - 1503 0.378 -0.542 1.299 8.446 2.643 1.16e-02 9.03e-02 -3.312 signal recognition particle subunit SRP54 SRP54
53 PF3D7_0324800 Pf3D7_03_v3 1027571 + 1359 -1.666 -2.748 -0.584 -0.333 -2.640 1.18e-02 9.06e-02 -2.780 rifin RIF
387 PF3D7_1218500 Pf3D7_12_v3 725841 - 3997 -0.424 -0.723 -0.126 9.347 -2.639 1.18e-02 9.06e-02 -3.335 conserved Plasmodium protein, unknown function NA
505 PF3D7_1404100 Pf3D7_14_v3 145134 - 516 -0.458 -1.116 0.200 5.102 -2.637 1.18e-02 9.06e-02 -3.085 cytochrome c, putative NA
199 PF3D7_0800300 Pf3D7_08_v3 40948 + 9992 -0.816 -1.213 -0.419 5.113 -2.638 1.18e-02 9.07e-02 -3.066 erythrocyte membrane protein 1, PfEMP1 VAR
190 PF3D7_0721600 Pf3D7_07_v3 931459 - 706 -0.412 -0.792 -0.031 10.693 -2.634 1.19e-02 9.09e-02 -3.360 40S ribosomal protein S5, putative NA
523 PF3D7_1417700 Pf3D7_14_v3 750330 + 1355 -0.499 -0.893 -0.105 4.889 -2.633 1.19e-02 9.10e-02 -3.061 conserved Plasmodium protein, unknown function NA
153 PF3D7_0624600 Pf3D7_06_v3 999524 + 8160 -0.447 -0.713 -0.182 10.780 -2.632 1.20e-02 9.11e-02 -3.365 SNF2 helicase, putative ISWI
564 PF3D7_1454300 Pf3D7_14_v3 2229284 + 2298 0.979 0.656 1.302 2.334 2.631 1.20e-02 9.11e-02 -2.866 serine/threonine protein kinase KIN KIN
48 PF3D7_0319500 Pf3D7_03_v3 815569 + 1287 -0.473 -0.827 -0.119 7.080 -2.627 1.21e-02 9.17e-02 -3.283 RNA-binding protein, putative NA
339 PF3D7_1122900 Pf3D7_11_v3 878969 + 16305 -0.879 -1.148 -0.609 1.460 -2.627 1.21e-02 9.17e-02 -2.849 dynein heavy chain, putative NA
462 PF3D7_1334200 Pf3D7_13_v3 1398271 + 1575 0.506 -0.050 1.063 6.071 2.627 1.21e-02 9.17e-02 -3.195 chaperone binding protein, putative NA
97 PF3D7_0511500 Pf3D7_05_v3 486602 + 30186 -0.607 -1.610 0.395 10.868 -2.629 1.22e-02 9.17e-02 -3.376 RNA pseudouridylate synthase, putative NA
513 PF3D7_1412100 Pf3D7_14_v3 484438 + 2871 1.011 0.085 1.937 2.315 2.626 1.21e-02 9.17e-02 -2.869 conserved Plasmodium protein, unknown function NA
172 PF3D7_0708400 Pf3D7_07_v3 381592 + 3023 -0.372 -0.756 0.012 12.204 -2.624 1.22e-02 9.17e-02 -3.373 heat shock protein 90 HSP90
207 PF3D7_0807600 Pf3D7_08_v3 389596 - 4664 -0.388 -0.885 0.109 9.522 -2.621 1.23e-02 9.22e-02 -3.385 conserved Plasmodium protein, unknown function NA
269 PF3D7_0934500 Pf3D7_09_v3 1350836 - 1094 -0.372 -0.695 -0.048 6.863 -2.618 1.24e-02 9.28e-02 -3.286 V-type proton ATPase subunit E, putative NA
369 PF3D7_1205400 Pf3D7_12_v3 232389 - 3258 1.011 0.447 1.576 3.919 2.617 1.25e-02 9.35e-02 -3.007 kelch domain-containing protein, putative NA
252 PF3D7_0914700 Pf3D7_09_v3 630657 + 1551 0.831 -0.152 1.814 6.915 2.619 1.26e-02 9.38e-02 -3.290 major facilitator superfamily-related transporter, putative MFR4
290 PF3D7_1015800 Pf3D7_10_v3 633682 + 1605 0.956 0.355 1.557 0.399 2.612 1.26e-02 9.38e-02 -2.846 ribonucleoside-diphosphate reductase small chain, putative NA
511 PF3D7_1410000 Pf3D7_14_v3 392972 - 879 0.428 -0.401 1.257 6.119 2.608 1.27e-02 9.46e-02 -3.248 ER membrane protein complex subunit 2, putative EMC2
47 PF3D7_0318900 Pf3D7_03_v3 791840 - 1642 -0.368 -1.187 0.450 5.696 -2.605 1.28e-02 9.47e-02 -3.206 conserved protein, unknown function NA
196 PF3D7_0724300 Pf3D7_07_v3 1021508 + 1123 0.774 0.112 1.437 1.018 2.604 1.28e-02 9.47e-02 -2.873 3-demethylubiquinone-9 3-methyltransferase, putative COQ3
251 PF3D7_0914300 Pf3D7_09_v3 612976 - 2517 0.367 -0.685 1.419 6.852 2.606 1.28e-02 9.47e-02 -3.314 met-10+ like protein, putative NA
388 PF3D7_1223300 Pf3D7_12_v3 934971 - 3669 0.474 -0.391 1.339 4.880 2.605 1.28e-02 9.47e-02 -3.115 DNA gyrase subunit A GyrA
259 PF3D7_0923000 Pf3D7_09_v3 939580 - 1008 0.392 -0.117 0.900 6.135 2.603 1.28e-02 9.47e-02 -3.251 DNA-directed RNA polymerase II subunit RPB3, putative RPB3
38 PF3D7_0308900 Pf3D7_03_v3 379130 - 4161 -0.402 -0.629 -0.176 8.929 -2.602 1.29e-02 9.50e-02 -3.419 splicing factor 3B subunit 1, putative SF3B1
219 PF3D7_0820800 Pf3D7_08_v3 936426 - 2451 0.882 0.384 1.379 0.753 2.598 1.30e-02 9.54e-02 -2.875 conserved Plasmodium protein, unknown function NA
242 PF3D7_0905800 Pf3D7_09_v3 289050 + 3848 0.418 -1.178 2.014 6.548 2.599 1.30e-02 9.54e-02 -3.297 conserved Plasmodium protein, unknown function NA
102 PF3D7_0516600 Pf3D7_05_v3 686810 - 4833 0.775 0.169 1.382 5.100 2.594 1.32e-02 9.57e-02 -3.149 sporozoite surface antigen MB2 MB2
115 PF3D7_0522800 Pf3D7_05_v3 944184 - 748 -0.415 -0.745 -0.085 6.133 -2.594 1.31e-02 9.57e-02 -3.268 pre-mRNA-splicing factor BUD31, putative BUD31
140 PF3D7_0608200 Pf3D7_06_v3 341874 - 948 -0.767 -1.230 -0.303 1.094 -2.593 1.32e-02 9.57e-02 -2.896 conserved Plasmodium protein, unknown function NA
158 PF3D7_0628700 Pf3D7_06_v3 1183896 + 1722 0.654 0.331 0.978 2.910 2.592 1.32e-02 9.57e-02 -2.973 conserved Plasmodium protein, unknown function NA
224 PF3D7_0822500 Pf3D7_08_v3 992655 - 1311 0.743 0.249 1.236 3.613 2.596 1.31e-02 9.57e-02 -3.013 dynein light chain 1 DLC1
356 PF3D7_1139700 Pf3D7_11_v3 1582995 - 1518 0.857 0.217 1.498 0.400 2.593 1.32e-02 9.57e-02 -2.879 adrenodoxin reductase, putative NA
521 PF3D7_1417200 Pf3D7_14_v3 694585 + 13593 -0.389 -0.834 0.055 9.868 -2.592 1.32e-02 9.57e-02 -3.451 NOT family protein, putative NA
50 PF3D7_0319900 Pf3D7_03_v3 833833 - 945 0.660 0.179 1.142 3.869 2.590 1.33e-02 9.57e-02 -3.053 conserved Plasmodium protein, unknown function NA
320 PF3D7_1104800 Pf3D7_11_v3 207440 + 2293 -0.691 -1.339 -0.042 3.529 -2.590 1.33e-02 9.57e-02 -3.089 metabolite/drug transporter, putative NA
425 PF3D7_1250900 Pf3D7_12_v3 2083353 - 966 0.877 -0.398 2.153 1.962 2.589 1.33e-02 9.57e-02 -2.934 conserved Plasmodium protein, unknown function NA
456 PF3D7_1327600 Pf3D7_13_v3 1159366 + 615 0.947 -0.145 2.039 2.094 2.591 1.33e-02 9.57e-02 -2.935 nicotinate-nucleotide adenylyltransferase NMNAT
20 PF3D7_0208300 Pf3D7_02_v3 337558 + 5409 0.654 -0.021 1.329 4.892 2.582 1.36e-02 9.74e-02 -3.174 conserved Plasmodium protein, unknown function NA
111 PF3D7_0520400 Pf3D7_05_v3 839655 - 906 0.813 0.084 1.542 2.273 2.580 1.36e-02 9.74e-02 -2.965 conserved Plasmodium protein, unknown function NA
458 PF3D7_1330700 Pf3D7_13_v3 1290118 + 2837 0.982 0.075 1.890 0.959 2.580 1.36e-02 9.74e-02 -2.919 GPI transamidase subunit PIG-U, putative NA
476 PF3D7_1350300 Pf3D7_13_v3 2011168 + 918 -0.573 -1.138 -0.008 5.457 -2.575 1.38e-02 9.85e-02 -3.230 conserved Plasmodium protein, unknown function NA
21 PF3D7_0208400 Pf3D7_02_v3 343308 - 6033 -0.376 -0.892 0.140 6.534 -2.573 1.39e-02 9.88e-02 -3.360 conserved Plasmodium protein, unknown function NA
41 PF3D7_0314400 Pf3D7_03_v3 579539 - 927 -0.535 -1.108 0.039 5.825 -2.568 1.40e-02 9.91e-02 -3.313 serine/threonine protein phosphatase 6, putative PPP6
42 PF3D7_0315800 Pf3D7_03_v3 641482 - 1098 0.457 -0.449 1.363 5.708 2.570 1.40e-02 9.91e-02 -3.281 zinc finger protein, putative NA
210 PF3D7_0811100 Pf3D7_08_v3 557884 - 1623 0.946 0.129 1.762 0.493 2.570 1.40e-02 9.91e-02 -2.931 mitochondrial carrier protein, putative NA
463 PF3D7_1336200 Pf3D7_13_v3 1474274 + 1388 -1.121 -1.435 -0.807 1.096 -2.569 1.40e-02 9.91e-02 -2.944 conserved Plasmodium protein, unknown function NA
577 PF3D7_1467500 Pf3D7_14_v3 2755225 + 1575 -0.339 -0.746 0.067 6.555 -2.568 1.40e-02 9.91e-02 -3.373 DNA/RNA-binding protein KIN17, putative NA

Heatmap of deregulated genes

col_annot <- data.frame(row.names = colnames(v$E), stringsAsFactors = F)
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "I"] <- "non-severe"
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "S"] <- "severe"
col_annot$phenotype <- as.factor(col_annot$phenotype)

pheatmap(v2$E[rownames(v$E) %in% top_ring_ruv$GeneID, ], show_rownames = FALSE, scale = "row", annotation_col = col_annot, annotation_colors = list(phenotype = c(`non-severe` = colors[1], 
    severe = colors[2])))

Gene sets from Daily et al and Shock et al

We now test using roast and camera for deregulation of gene sets obtained from the papers:

Daily, J. P., D. Scanfeld, N. Pochet, K. Le Roch, D. Plouffe, M. Kamal, O. Sarr, et al. 2007. “Distinct Physiological States of Plasmodium Falciparum in Malaria-Infected Patients.” Nature 450 (7172): 1091–95.

Shock, Jennifer L., Kael F. Fischer, and Joseph L. DeRisi. 2007. “Whole-Genome Analysis of mRNA Decay in Plasmodium Falciparum Reveals a Global Lengthening of mRNA Half-Life during the Intra-Erythrocytic Development Cycle.” Genome Biology 8 (7): R134.

setwd(wd)

# Load gene lists from Daily et al and Shock et al
daily_figure2 <- fread("./data/daily_expression_figure2.csv", data.table = FALSE, header = TRUE)

JLshock <- c("PF3D7_0320800", "PF3D7_0410400", "PF3D7_0507600", "PF3D7_0520300", "PF3D7_0720000", "PF3D7_0811300", "PF3D7_0819900", "PF3D7_0909400", "PF3D7_0909900", 
    "PF3D7_1006100", "PF3D7_1032100", "PF3D7_1103800", "PF3D7_1106300", "PF3D7_1107000", "PF3D7_1124400", "PF3D7_1128600", "PF3D7_1209200", "PF3D7_1224300", 
    "PF3D7_1235300", "PF3D7_1307000", "PF3D7_1308900", "PF3D7_1325000", "PF3D7_1340100", "PF3D7_1364500", "PF3D7_1427800", "PF3D7_1443300", "PF3D7_1443500", 
    "PF3D7_1449700", "PF3D7_0519500")

# Load entrex geneID mappings
entrez_geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)

upcluster2 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "Y"]
upcluster1 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "N"]
glycolisis <- daily_figure2$Gene[daily_figure2$type == "Glycolisis"]
tricarboxylic <- daily_figure2$Gene[daily_figure2$type == "Tricarboxylic acid cycle"]
fatty_acid <- daily_figure2$Gene[daily_figure2$type == "Fatty acid metabolism"]

upcluster2 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster2])
upcluster1 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster1])
glycolisis <- as.vector(geneID_mappings$current[geneID_mappings$old %in% glycolisis])
tricarboxylic <- as.vector(geneID_mappings$current[geneID_mappings$old %in% tricarboxylic])
fatty_acid <- as.vector(geneID_mappings$current[geneID_mappings$old %in% fatty_acid])

indices <- ids2indices(list(up_in_starvation = upcluster1, up_int_vitro = upcluster2, glycolisis = glycolisis, tricarboxylic = tricarboxylic, fatty_acid = fatty_acid, 
    mRNA_degradation = JLshock), rownames(v2$E))
mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")
##                  NGenes  PropDown     PropUp Direction     PValue        FDR PValue.Mixed   FDR.Mixed
## mRNA_degradation     29 0.2758621 0.06896552      Down 0.00629937 0.02204780   0.00129987 0.004649535
## up_int_vitro         12 0.8333333 0.00000000      Down 0.00739926 0.02204780   0.00789921 0.011773823
## tricarboxylic        11 0.1818182 0.36363636        Up 0.01219878 0.02422258   0.00159984 0.004649535
## glycolisis           19 0.5263158 0.00000000      Down 0.01619838 0.02422258   0.01509849 0.015098490
## up_in_starvation     33 0.1515152 0.21212121        Up 0.03609639 0.04325567   0.00329967 0.006499350
## fatty_acid           17 0.1764706 0.17647059        Up 0.06279372 0.06279372   0.01259874 0.015048495
camera(v2, index = indices, design = modRUV, contrast = 2)
##                  NGenes Correlation Direction    PValue       FDR
## up_int_vitro         12  0.55011389      Down 0.1013887 0.4438285
## glycolisis           19  0.24854294      Down 0.1593857 0.4438285
## mRNA_degradation     29  0.06758603      Down 0.2219142 0.4438285
## tricarboxylic        11  0.06650577        Up 0.3661151 0.4725657
## up_in_starvation     33  0.07007488        Up 0.4263498 0.4725657
## fatty_acid           17  0.05459497        Up 0.4725657 0.4725657

KEGG analysis

# setwd(wd) entrez_de <- entrez_geneID_mappings$`[Entrez Gene ID]`[entrez_geneID_mappings$`[Gene ID]` %in% top_ring_ruv$GeneID] entrez_de <-
# entrez_de[entrez_de!='null'] entrez_de <- str_split_fixed(entrez_de, pattern = ',', n = 2)[,1] kegg <- kegga(entrez_de, species.KEGG='pfa',
# convert=TRUE) kable(topKEGG(kegg, n=Inf))

GO analysis

# go <- goana(entrez_de, species.KEGG='pfa', convert=TRUE) kable(topGO(go, n=100))

System Information

setwd(wd)
sessionInfo()
## R version 3.2.0 (2015-04-16)
## Platform: x86_64-apple-darwin15.4.0 (64-bit)
## Running under: OS X 10.11.4 (unknown)
## 
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] pheatmap_1.0.8             knitr_1.15.1               stringr_1.1.0              dplyr_0.5.0                data.table_1.10.0         
##  [6] VennDiagram_1.6.17         futile.logger_1.4.3        RColorBrewer_1.1-2         EDASeq_2.4.1               ShortRead_1.28.0          
## [11] GenomicAlignments_1.6.3    SummarizedExperiment_1.0.2 Rsamtools_1.22.0           GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        
## [16] Biostrings_2.38.4          XVector_0.10.0             IRanges_2.4.8              S4Vectors_0.8.11           BiocParallel_1.4.3        
## [21] Biobase_2.30.0             BiocGenerics_0.16.1        reshape2_1.4.2             ggplot2_2.2.1              ruv_0.9.6                 
## [26] quadprog_1.5-5             edgeR_3.12.1               limma_3.26.9              
## 
## loaded via a namespace (and not attached):
##  [1] splines_3.2.0           R.utils_2.5.0           assertthat_0.1          statmod_1.4.27          highr_0.6               aroma.light_3.0.0      
##  [7] latticeExtra_0.6-28     yaml_2.1.14             RSQLite_1.1-1           backports_1.0.4         lattice_0.20-31         digest_0.6.11          
## [13] colorspace_1.3-2        htmltools_0.3.5         Matrix_1.2-0            R.oo_1.21.0             plyr_1.8.4              XML_3.98-1.5           
## [19] biomaRt_2.26.1          genefilter_1.52.1       zlibbioc_1.16.0         xtable_1.8-2            scales_0.4.1            tibble_1.2             
## [25] annotate_1.48.0         GenomicFeatures_1.22.13 lazyeval_0.2.0          survival_2.40-1         magrittr_1.5            memoise_1.0.0          
## [31] evaluate_0.10           R.methodsS3_1.7.1       hwriter_1.3.2           tools_3.2.0             formatR_1.4             matrixStats_0.51.0     
## [37] munsell_0.4.3           AnnotationDbi_1.32.3    lambda.r_1.1.9          DESeq_1.22.1            RCurl_1.95-4.8          bitops_1.0-6           
## [43] labeling_0.3            rmarkdown_1.3           gtable_0.2.0            DBI_0.5-1               R6_2.2.0                rtracklayer_1.30.4     
## [49] rprojroot_1.1           futile.options_1.0.0    stringi_1.1.2           Rcpp_0.12.8             geneplotter_1.48.0